"ALPHASIM_01"

REST, SPM

"CELLQUEST_01"

Autodock Vina, CompuSin, CompuSyn, InsightII, Linux Red Hat, Prism, PyMOL, Quantity One, Vina

"CHART_01"

CANTAB, STATA

"CIMSIM_01"

Skeeter Buster

"DATACAM_01"

Excel, Mac, SPSS

"DIGIPRO_01"

SPSS, Scion image

"DRAEGER_EIT_DATA_ANALYSIS_TOOL_01"

SPSS

"EASY_RA1_EASY_RANDOMIZER_01"

Excel, PowerPoint, SAS

"EXPERIMENT_CENTER_01"

BeGaze, G*Power, iView X

"EYELINK_API_01"

Matlab

"EYEVISION_01"

SPSS

"GLOBALPARK_01"

Excel, SNAP, SPSS Dimensions

"HABIT_2000_01"

TouchStat, VPixx

"HGF_01"

Matlab, Psychophysics Toolbox, SPM, SPSS, TAPAS, Windows

"IMAGELAB_01"

SPSS Statistics, Windows

"IVIEW_X_01"

BeGaze, Experiment Center, G*Power

"LSM_IMAGING_01"

Chromeleon, Openlab

"SADABS_01"

AMBERTOOLS, CPPTRAJ, Chimera, MOE, ORTEP, PASS, SAINT, SHELXTL

"SAINT_01"

AMBERTOOLS, CPPTRAJ, Chimera, MOE, ORTEP, PASS, SADABS, SHELXTL

"SNAP_01"

Excel, Globalpark, SPSS Dimensions

BD FACSDiva, Cufflinks, Cytoscape, DAVID, FastQC, GSEA-P, Tophat, iGenomes

Image lab, ModFit, PPI Network, SPSS, TargetScan, Venny, Xena, miRDB, microRNA

BioMart, Ensembl, MAGMA

CADD, GATK, Geneious, Genome Analysis Toolkit, ImageJ, Novoalign, Polyphen, Prism, Sift, VAX

Java, Perl, SQL, UNIX

JAVA, Java, Java Runtime Environment, Java Virtual Machine, Windows

R

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

BWA, DESeq, FIMO, HTSeq, KOBAS, MACS, Perl, R, TopHat, skewer

C, C++

TreeDyn

FACSuite, Prism, cellSens Dimension

BioConductor, Bioanalyzer, CASAVA, CIBERSORT, DESeq2, EdgeR, FlowJo, GSEA, Genepix Pro, Image-Pro Plus, J-Express, LAS, PIVOT, Prism, R, RSeQC, RTA, Rtsne, SAS, STAR, Sailfish, Subread, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

Trimmomatic

LI-toolbox, MATLAB, Macintosh, Presentation, SPM, SPM anatomy toolbox, SPSS, SPSS Statistics, WFU-Pickatlas

C2, Mimics, R, Strand7, clam, rioja

CloVR-ITS

Linux, Windows

Netcdf, NumPy, Pycdf, Pycluster, Python, matplotlib, tcl, tk

BLAST, Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FastQC, FlowJo, Gene Cluster, Genepix Pro, IPA, Mirdeep2, PIVOT, Primer-BLAST, Prism, R, RSeQC, RTA, Rtsne, SPSS, Sailfish, Samtools, Subread, TargetScan, ToppFun, TreeView, Treeview, Trimmomatic, edge, edgeR, gplots, immunoSEQ Analyzer, miRDB, vegan

Blastn, DNAsp, EstimateS, Geneious, MEGA, MUSCLE, PCORD, Perl, PyroTagger, RDP Classifier, blastn

C, Fortran, Linux, Mac, Windows

BEAGLE, GATK, GEMINI, Genome Variation Server, MERLIN, MORGAN, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, SLINK, Seattle Seq, Variant Effect Predictor, cnvHap, mrsFAST

DS ViewerPro, SHARP2

Linux, R, Windows, gdata, gplots, gtools, hgu95av2, hu6800, linux, plotrix, windows

BEAGLE, CoNIFER, GATK, GEMINI, Genome Variation Server, MERLIN, MORGAN, PBAP, PLINK, PennCNV, PolyPhen, SLINK, Seattle Seq, Variant Effect Predictor, cnvHap, mrsFAST

BeadStudio, Birdseye, GRIMP, METAL, Mach2QTL, PLINK, SPSS Statistics

BOLT-LMM, BeadStudio, DISSECT, GRIMP, GTX, GenCall, HRC, IMPUTE, KING, METACARPA, Mach, Mach2QTL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, SNPTEST, SPSS Statistics, ordinal, rms

BioMart, Ensembl, GREAT

FixErrors, MATLAB, Matlab

Ctrax, MATLAB

BD FACSDiva, BisoGenet, Cufflinks, Cytoscape, FastQC, GSEA-P, Tophat, iGenomes

BD FACSDiva, BisoGenet, Cufflinks, Cytoscape, DAVID, FastQC, GSEA-P, Tophat, iGenomes

ARLEQUIN, Arlequin, BEAST, BIOEDIT, BLAST, Bioportal, Bottleneck, CLUMPP, Clustal W, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FAP, FREENA, FSTAT, Fig Tree, Fstat, GENELAND, GENEPOP, GenePop, Geneland, Google Earth, IBDWS, LAGRANGE, LogCombiner, MCMCglmm, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, Modeltest, MrBayes, NETWORK, Network, PAUP, PAUP*, PHASE, PhyML, R, SPAGeDI, SPLITSTREE, STRUCTURE, Structure, TRACER, Tracer, TreeAnnotator, VIP, beast, car, convert, lme4, migrate

Java

C, C++, Objective-C, OsiriX, dcm4che, dcm4chee

Matlab, SPM

Attivio, Inxight, NLTK, Python, Yahoo-BOSS, Yahoo-BOSS API

GNU R, Python, READ, samtools, vcftools

C#, Windows

Mac, Windows

ArcView, BLAST, MEGA, SPSS

ASCAT, BEAGLE, BLAST, CADD, ChAMP, CoNIFER, Condel, GATK, GEMINI, Geneious, Genome Analysis Toolkit, Genome Variation Server, Genome browser, GenomeStudio, ImageJ, MERLIN, MORGAN, MSIsensor, MuPeXI, MuTect, Mutation Surveyor, MutationAssessor, MutationalPatterns, NetMHCpan, Novoalign, PBAP, PEDSTATS, PLINK, PennCNV, Picard, Polysolver, Primer, Prism, R, REDCap, RTN, SLINK, Salmon, Seattle Seq, Sift, SnpEff, SomaticSignatures, Trim Galore!, VAX, VarScan, Variant Effect Predictor, Visiopharm, bam-readcount, bcl2fastq2, cnvHap, consensus MIBC, edgeR, mrsFAST, samtools, survival, survminer, tximport, xCell

Python

BioPython, IDEPI, Python, VirtualBox, joblib, scikit-learn

Structure

Arlequin, BLAST, Bottleneck, Clustal W, DnaSP, EXCEL, Fig Tree, Fstat, GenePop, Geneland, Google Earth, IBDWS, LogCombiner, MEGA, Modeltest, MrBayes, Network, PAUP*, Structure, Tracer, TreeAnnotator, beast, genemapper, migrate

Image J, NIS, SPSS

BioNetGen, CVODE, MatCont, RuleBender, SUNDIALS

NCSS

Stata

Habit 2000, VPixx

BioConductor, Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, GSEA, Gene Cluster, Genepix Pro, Image-Pro Plus, J-Express, LAS, PIVOT, Prism, R, RSeQC, RTA, Rtsne, SAS, STAR, Sailfish, Subread, ToppFun, immunoSEQ Analyzer

FigureJ, ImageJ, Java, Ki67 Vv, R, ROCR

BWA, DESeq, FIMO, GOseq, HTSeq, MACS, Perl, R, TopHat, skewer

CIMSiM

BWA, DESeq, FIMO, GOseq, HTSeq, KOBAS, Perl, R, TopHat, skewer

C, Linux, NovoSNP, Perl, PolyPhred, Unix

E-Prime, GoldWave, Pickatlas, Presentation, SPM, SPSS, WFU-pick atlas

ENCORE, Python

BWA, DESeq, GOseq, HTSeq, KOBAS, MACS, Perl, R, TopHat, skewer

BLAST, FastQC, IPA, Image lab, MCODE, Mirdeep2, ModFit, PPI Network, Primer-BLAST, R, SPSS, STAR, Samtools, TargetScan, Trimmomatic, Venny, Xena, edge, edgeR, gplots, microRNA, vegan

MSACompro

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

BrainStorm, MATLAB, R, Scan, openMEEG

C, Linux, Perl, PolyPhred, SNPdetector, Unix

BLAST, ClustalW, I-TASSER, MASCOT, Muscle, PhyML, SMART, SPSS, SignalP

Protégé

BrainStorm, LAN toolbox, MATLAB, R, Scan

Linux, MacOS X, PyPi, Python, Qt, Ubuntu, Windows

BEAGLE, CoNIFER, GATK, GEMINI, Genome Variation Server, MERLIN, MORGAN, PBAP, PEDSTATS, PLINK, PolyPhen, SLINK, Seattle Seq, Variant Effect Predictor, cnvHap, mrsFAST

Linux, Mac OS X, Python, Windows

Linux, MIiSR, Macintosh, Matlab, QuickPALM, Windows

Python

Matlab

Brainsight, Matlab, Psychtoolbox

Psychophysics Toolbox

Bellerpheron, Blastn, DNAsp, EstimateS, Geneious, MEGA, MUSCLE, PCORD, Perl, RDP Classifier, blastn

Crimap, R/Qtl, qxpak

Bellerpheron, Blastn, DNAsp, EstimateS, Geneious, MEGA, MUSCLE, PCORD, Perl, PyroTagger, blastn

Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RTA, Rtsne, STAR, Sailfish, Subread, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

BEAGLE, CoNIFER, GATK, GEMINI, Genome Variation Server, MERLIN, MORGAN, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, SLINK, Seattle Seq, Variant Effect Predictor, cnvHap

BLAST, ClustalW, GlobalWorks, I-TASSER, MASCOT, Muscle, PhyML, SPSS, SignalP

ImageJ, Java, Java Advanced Imaging

ARLEQUIN, BEAST, BIOEDIT, Bioportal, CLUMPP, DISTRUCT, DIYABC, Datamonkey, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, LAGRANGE, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, NETWORK, PAUP, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, TRACER, VIP

Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RSeQC, RTA, Rtsne, STAR, Sailfish, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

Bioanalyzer, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RSeQC, RTA, Rtsne, STAR, Sailfish, Subread, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

MSAProbs

QTL Express, R/Qtl, qxpak

BiNGO, ClueGO, Cytoscape, FunRich, MASCOT, Office Excel, Prism, Reactome, clusterMaker, cytoscape

FDT, FSL, Stata

ARLEQUIN, Arlequin, BEAST, BIOEDIT, BLAST, Bioportal, Bottleneck, CLUMPP, Clustal W, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FREENA, FSTAT, Fig Tree, Fstat, GENELAND, GENEMAPPER, GENEPOP, GenePop, Geneland, Google Earth, IBDWS, LAGRANGE, LogCombiner, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, Modeltest, MrBayes, NETWORK, Network, PAUP, PAUP*, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, Structure, TreeAnnotator, VIP, beast, convert, genemapper, migrate

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

GNU R, GRAB, Python, READ, samtools

CellQuest, CompuSin, CompuSyn, InsightII, Linux Red Hat, Prism, PyMOL, Quantity One

AUTO, BioNetGen, CVODE, MatCont, SUNDIALS

C++, Linux, Mac, Windows

R, T-LoCoH, boot

Visual Basic, Window, Windows

ConSurf-HSSP, SHARP2

SAS

IPP, Image-Pro Plus, Office Excel, Photoshop, Satistix, SigmaPlot, SigmaStat, Windows

GeneMapper, MCMCglmm, R, car, lme4

AFNI, FSL, ISC-toolbox, MATLAB, Psychophysics Toolbox, SPM

ARLEQUIN, BEAST, BIOEDIT, BLAST, Bioportal, CLUMPP, ClustalW, DISTRUCT, DIYABC, Datamonkey, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, GlobalWorks, I-TASSER, LAGRANGE, MASCOT, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, Muscle, NETWORK, PAUP, PHASE, SMART, SPAGeDI, SPLITSTREE, SPSS, STRUCTURE, SignalP, TRACER, VIP

MATLAB, Praat, articulatory synthesizer

BLASR, C++, Linux, Perl

Image Processing Toolbox, Linux, MacOSX, Matlab, Windows

CLC Genomic Workbench, Newbler, Novoalign, Python, SAMtools, SMRT analysis, github

ConSurf-HSSP, DS ViewerPro

Java

ARLEQUIN, BEAST, BIOEDIT, CLUMPP, DISTRUCT, DIYABC, Datamonkey, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, LAGRANGE, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, NETWORK, PAUP, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, TRACER, VIP

BrainVoyager, MATLAB

Stata

MLWiN, MLwiN, STATA, Stata

Java

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

BLAST, ClustalW, GlobalWorks, I-TASSER, MASCOT, Muscle, PhyML, SMART, SPSS

Linux, Windows

MATLAB

AMBERTOOLS, CPPTRAJ, MOE, ORTEP, PASS, SADABS, SAINT, SHELXTL

Sailfish

C, C++, gcc, linux

AMIX, Chenomx, Chenomx NMR Suite, Fiji, ImageJ, Prism, Quantity One, Rotor-Gene Q, SIMCA-P, TopSpin

IDL, IDL Virtual Machine, Windows

BOLT-LMM, GTX, GenCall, HRC, IMPUTE, KING, METACARPA, METAL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, SNPTEST, ordinal, rms

C, PERL

MATLAB, SPSS

BioMart, DS modeling, GREAT, Image J, MAGMA, Primer3 Input, Q-LAB, pCLAMP

excel

COLONY, SAS

ImageJ, Immunoratio, Java, Ki67 Vv, R, ROCR

BiNGO, Bioworks, ClueGO, Cytoscape, MASCOT, Office Excel, Prism, Reactome, clusterMaker, cytoscape

GAMESS

ImagePro+, MyIQ, STATA

BOLT-LMM, DISSECT, GTX, GenCall, IMPUTE, KING, METACARPA, METAL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, SNPTEST, ordinal, rms

AMBERTOOLS, CPPTRAJ, Chimera, MOE, ORTEP, SADABS, SAINT, SHELXTL

ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

BEAGLE, CoNIFER, GATK, GEMINI, Genome Variation Server, MERLIN, MORGAN, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, SLINK, Seattle Seq, Variant Effect Predictor, mrsFAST

Attivio, NLTK, Python, Yahoo-BOSS, Yahoo-BOSS API

2LD, CLUMP, GENEPOP, Haploview, MassARRAY Assay Design, MassARRAY Typer, PGA, windows

Biotrace, MATLAB, Psychtoolbox

ARLEQUIN, BEAST, BIOEDIT, Bioportal, CLUMPP, DISTRUCT, DIYABC, Datamonkey, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, LAGRANGE, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, NETWORK, PAUP, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, TRACER

Actionscript, Flash, Matlab

C++

Stata

Image lab, MCODE, ModFit, PPI Network, SPSS, TargetScan, Venny, Xena, miRDB

Stata

GraphPad, MATLAB, Open sorter

ART, FSL, SPM

CADD, CLC Genomic Workbench, Condel, GARLI, GATK, Geneious, Genome Analysis Toolkit, ImageJ, Newbler, Polyphen, Prism, Python, SAMtools, SMRT analysis, Sift, VAX, github

ARLEQUIN, BEAST, BIOEDIT, BOTTLENECK, Bioportal, CLUMPP, COANCESTRY, COLONY, DISTRUCT, DIYABC, Datamonkey, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, GenAlEx, Genescan, LAGRANGE, MEGA, MLRELATE, MODELTEST, MRBAYES, NETWORK, PAUP, PHASE, Peakscanner, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, TRACER, VIP

DTIFit, FLIRT, FMRIB Software Library, FNIRT, FSL, FSL-VBM, MELODIC, SPSS, TBSS, VBM, dual regression

CBFA, GLPK, JDK, Java, Java JRE, Mac OS

GLPK, JDK, Java, Java JRE, Mac OS, OptFlux, Optflux

Linux, Macintosh, Matlab, QuickPALM, Windows

Chrome, Django, Firefox, HTML, Internet Explorer, Python, R, Safari, VirtualBox, jQuery

Java

ArcGIS, Bellerpheron, Blastn, DNAsp, Geneious, MEGA, MUSCLE, PCORD, Perl, Photofiltre, PyroTagger, R, RDP Classifier, blastn, lme4

AlphaSim, SPM

ConQuest, IPA, Plink, R, eRM, ltm

ENMtools, Google Earth, MaxEnt

R, SAS

Artemis, BLASTp, BioTools, Flex Analysis, InterPro, MASCOT, PhylopythiaS, ProteomeWeaver, SigmaPlot, SigmaStat

ArcGIS, ENVI, Fragstats, STATA, Spatial Statistics

ArcGis, Maxent, Spatial Analyst

BEAGLE, CoNIFER, GATK, GEMINI, Genome Variation Server, MORGAN, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, SLINK, Seattle Seq, Variant Effect Predictor, cnvHap, mrsFAST

BrainVoyager, DARTEL, SPM, SPSS Statistics, WFU pickatlas

Google Cloud, Matlab

EEGLab, Excel, MATLAB, SPSS, WinEEG, sLORETA

Acrobat, FlowJo, Statview

OHM

Arlequin, BLAST, Bellerpheron, Blastn, Bottleneck, Clustal W, EXCEL, EstimateS, Fig Tree, Fstat, GenePop, Geneious, Geneland, Google Earth, IBDWS, LogCombiner, MEGA, MUSCLE, Modeltest, MrBayes, Network, PAUP*, PCORD, Perl, PyroTagger, RDP Classifier, Structure, Tracer, TreeAnnotator, beast, blastn, convert, genemapper, migrate

ArcGIS, ENVI, STATA, Spatial Statistics

MetaMorph, Primer, SPSS, Virtuoso, Volume 1

MultiPak, iTeva

Igor pro, Photoshop, Visilog, pClamp

3dClustsim, 3dDeconvolve, 3dDetrend, 3dFWHMx, 3dmaskave, 3dttest+ +, AFNI, Matlab, SPSS, waver

MATLAB

DTV.II SR, MetaMorph, Primer, SPSS, Virtuoso

Image lab, MCODE, PPI Network, SPSS, TargetScan, Venny, Xena, miRDB, microRNA

Praat

GraphPad, IMARIS, ImageJ

MATLAB

ARLEQUIN, BEAST, BIOEDIT, Bioportal, CLUMPP, DISTRUCT, Datamonkey, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, LAGRANGE, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, NETWORK, PAUP, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, TRACER, VIP

Arlequin, BLAST, COANCESTRY, COLONY, Clustal W, DnaSP, EXCEL, Fig Tree, Fstat, GENEPOP, GenAlEx, GenePop, Geneland, Genescan, Google Earth, IBDWS, LogCombiner, MEGA, MICROCHECKER, MLRELATE, Modeltest, MrBayes, Network, PAUP*, Peakscanner, Structure, Tracer, TreeAnnotator, beast, convert, genemapper, migrate

GenePix, ImaGene

SPM

C#, Windows

Matlab

Epidata, Stata

EXCEL, SPSS

3dBandpass, 3dDespike, AFNI, BootES, Debian, FreeSurfer, MSM-All, MapIcosahedron, NeuroDebian, NeuroSynth, PyMVPA

3dDespike, AFNI, BootES, Debian, FreeSurfer, MSM-All, MapIcosahedron, NeuroDebian, NeuroSynth, PyMVPA, SUMA

3dDeconvolve, 3dDetrend, 3dFWHMx, 3dmaskave, 3dttest+ +, AFNI, Cogent, Matlab, SPSS, waver

3dClustsim, 3dDetrend, 3dFWHMx, 3dmaskave, 3dttest+ +, AFNI, Cogent, Matlab, SPSS, waver

3dBandpass, AFNI, BootES, Debian, FreeSurfer, MSM-All, MapIcosahedron, NeuroDebian, NeuroSynth, PyMVPA, SUMA

3dClustsim, 3dDeconvolve, 3dFWHMx, 3dmaskave, 3dttest+ +, AFNI, Cogent, Matlab, SPSS, waver

AFNI, EyeLink Data Viewer, Matlab, Python, SPSS, iMap

3dClustsim, 3dDeconvolve, 3dDetrend, 3dmaskave, 3dttest+ +, AFNI, Cogent, Matlab, SPSS, waver

3dClustsim, 3dDeconvolve, 3dDetrend, 3dFWHMx, 3dttest+ +, AFNI, Cogent, Matlab, SPSS, waver

3dClustsim, 3dDeconvolve, 3dDetrend, 3dFWHMx, 3dmaskave, AFNI, Cogent, Matlab, SPSS, waver

3dBandpass, 3dDespike, AFNI, BootES, Debian, FreeSurfer, MSM-All, NeuroDebian, NeuroSynth, PyMVPA, SUMA

3dClustsim, 3dDeconvolve, 3dDetrend, 3dFWHMx, 3dmaskave, 3dttest+ +, AFNI, Cogent, Matlab, SPSS

2LD, CLUMP, GENECOUNTING, GENEPOP, Haploview, PGA, windows

DISSECT, GTX, GenCall, HRC, IMPUTE, KING, METACARPA, METAL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, SNPTEST, ordinal, rms

Aninhado, Pajek, R, bipartite

CPPTRAJ, Chimera, MOE, ORTEP, PASS, SADABS, SAINT, SHELXTL

Netcdf, NumPy, PyMS, Pycdf, Python, matplotlib, tcl, tk

BiNGO, Bioworks, Cytoscape, FunRich, MASCOT, Office Excel, Prism, Reactome, clusterMaker, cytoscape

BiNGO, Bioworks, ClueGO, Cytoscape, FunRich, MASCOT, Office Excel, Prism, Reactome, cytoscape

BiNGO, Bioworks, ClueGO, Cytoscape, FunRich, MASCOT, Office Excel, Prism, clusterMaker, cytoscape

ANNOVAR, BCFtools, BWA-MEM, CNVmap, GATK, GeneOverlap, PLINK, Picard, R, SAMtools, XHMM, bedtools, cutadapt, sickle

ARLEQUIN, Arlequin, BIOEDIT, BLAST, Bioportal, Bottleneck, CLUMPP, Clustal W, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FREENA, FSTAT, Fig Tree, Fstat, GENELAND, GENEMAPPER, GENEPOP, GenePop, Geneland, GitHub, Google Earth, IBDWS, LAGRANGE, LogCombiner, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, Modeltest, MrBayes, MultiTypeTree, NETWORK, Network, PAUP, PAUP*, PHASE, PhyML, SCOTTI, SPAGeDI, SPLITSTREE, STRUCTURE, Structure, TRACER, Tracer, TreeAnnotator, VIP, convert, genemapper, migrate

Arlequin, BLAST, Bottleneck, Clustal W, DnaSP, EXCEL, Fig Tree, Fstat, GenePop, Geneland, Google Earth, IBDWS, MEGA, Modeltest, MrBayes, Network, PAUP*, Structure, Tracer, TreeAnnotator, beast, convert, genemapper, migrate

C++, Cluster, DriverNet, FunciSNP, GSEA, Image-Pro Plus, J-Express, LAS, R, Rcpp, Rhtslib, SAS, TreeView, illuminaio, scPipe

ASCAT, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

BWA, FIMO, GOseq, HTSeq, KOBAS, MACS, Perl, R, TopHat, skewer

Bioanalyzer, CASAVA, CIBERSORT, Cluster, EdgeR, FlowJo, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RSeQC, RTA, Rtsne, STAR, Sailfish, Subread, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

Bioconductor, R

Bioconductor, R

ANNOVAR, BCFtools, BWA-MEM, CNVmap, GATK, PLINK, PLINK/SEQ, Picard, R, SAMtools, XHMM, bedtools, cutadapt, sickle

Analyst, BLASTp, Bioplex Manager, Epi, R, Skyline

Bioconductor, C++, R, Rcpp, scPipe

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

ASCAT, BLAST, Bioanalyzer, CASAVA, CIBERSORT, ChAMP, Cluster, DESeq2, FastQC, FlowJo, GATK, Gene Cluster, Genepix Pro, GenomeStudio, IPA, MSIsensor, Mirdeep2, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, PIVOT, Picard, PolyPhen, Polyphen, Polysolver, Primer-BLAST, Prism, R, REDCap, RSeQC, RTA, RTN, Rtsne, SPSS, STAR, Sailfish, Salmon, Samtools, SnpEff, SomaticSignatures, Subread, TargetScan, ToppFun, TreeView, Treeview, Trim Galore!, Trimmomatic, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edge, gplots, immunoSEQ Analyzer, miRDB, samtools, survival, survminer, tximport, vegan, xCell

CoXpress, Linux, R, Windows, coXpress, gdata, gplots, gtools, hu6800, linux, plotrix, windows

CoXpress, Linux, R, Windows, coXpress, gdata, gplots, gtools, hgu95av2, linux, plotrix, windows

Bioconductor, R

Bioconductor, C++, R, Rcpp, Rhtslib

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, xCell

Image lab, MCODE, MEGA, ModFit, Mothur, PPI Network, SILVA SINA, SPSS, TargetScan, Xena, miRDB, microRNA

Prism, Quantity One, SPSS

BOTTLENECK, COANCESTRY, COLONY, GENEPOP, Genescan, MICROCHECKER, MLRELATE, Peakscanner

Bitbucket

GNU R, GRAB, Python, samtools, vcftools

MATLAB

Artemis, BLASTp, FGENESB, Flex Analysis, InterPro, MASCOT, PhylopythiaS, ProteomeWeaver, SigmaPlot, SigmaStat

BEAGLE, CoNIFER, Condel, GATK, GEMINI, Geneious, Genome Analysis Toolkit, Genome Variation Server, ImageJ, MERLIN, MORGAN, Novoalign, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, Polyphen, Prism, SLINK, Seattle Seq, Sift, VAX, Variant Effect Predictor, cnvHap, mrsFAST

JavaScript, Python

Bioanalyzer, CASAVA, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RSeQC, RTA, Rtsne, STAR, Sailfish, Subread, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

ARLEQUIN, BEAST, BIOEDIT, Bioportal, CLUMPP, DISTRUCT, DIYABC, Datamonkey, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, NETWORK, PAUP, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, TRACER, VIP

Linux, MIiSR, Macintosh, Matlab, Windows

BrainStorm, LAN toolbox, MATLAB, R, openMEEG

MPlus, Mplus, Windows

Analyst, BLASTp, Bioplex Manager, MSstats, R, Skyline

FAP, GeneMapper, R, car, lme4

Blast, Primer, R

WinBugs

FigureJ, ImageJ, Immunoratio, Java, Ki67 Vv, R

Bioconductor, C++, R, Rhtslib, scPipe

Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RSeQC, RTA, STAR, Sailfish, Subread, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

CRAN, R

Aninhado, Pajek, R, netcarto

R

R, SOCPROG, T-LoCoH

3dBandpass, 3dDespike, AFNI, Debian, FreeSurfer, MSM-All, MapIcosahedron, NeuroDebian, NeuroSynth, PyMVPA, SUMA

FAP, GeneMapper, MCMCglmm, R, lme4

GSEA, PyRadiomics, TensorFlow, irr, mRMRe, survcomp

C2, CALIB, Calib, R, rioja

CRAN, GitHub, R

R

R Studio, SAS

ConQuest, IPA, Plink, R, RUMM, ltm

BioEdit, MEGA, QGIS, R, ggplot2, mgcv

R, SPSS

R

CoXpress, Linux, R, Windows, coXpress, gplots, gtools, hgu95av2, hu6800, linux, plotrix, windows

C++, OpenCL, R, Stata, Statistica, gpu-lasso

BLAST, CoXpress, FastQC, IPA, Linux, Mirdeep2, Primer-BLAST, R, SPSS, STAR, Samtools, TargetScan, Trimmomatic, Windows, coXpress, edge, edgeR, gdata, gtools, hgu95av2, hu6800, linux, miRDB, plotrix, vegan, windows

CoXpress, Linux, R, Windows, coXpress, gdata, gplots, hgu95av2, hu6800, linux, plotrix, windows

R, Windows, h2oEnsemble, pROC

GSEA, PyRadiomics, TensorFlow, caret, mRMRe, survcomp

Mice, R, Survival, mitml, survC1

ArcGIS, EstimateS, FAP, GeneMapper, MCMCglmm, Matlab, Mixer, Photofiltre, Photoshop, Pixelmator, R, Visual Basic, adjustedRandIndex, car

ConQuest, IPA, Plink, R, RUMM, eRM

GSEA, PyRadiomics, TensorFlow, caret, irr, survcomp

Matlab, Mixer, R, lmer

BioEdit, EpiR, GDAL, MEGA, QGIS, R, ggplot2, raster, rgdal

R, Soscisurvey, Survival, lattice, mitml, survC1

Mice, R, Survival, lattice, survC1

ImageJ, JMP, Macintosh, R, R Studio, SPSS, SPSS Statistics

BOLT-LMM, DISSECT, GTX, GenCall, HRC, IMPUTE, KING, METACARPA, METAL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, SNPTEST, rms

H2O R interface, R, Windows, h2oEnsemble

CoXpress, Linux, R, Windows, coXpress, gdata, gplots, gtools, hgu95av2, hu6800, linux, windows

Promasys, R, dplyr, tidyr

Crimap, QTL Express, qxpak

R

GDAL, R, mgcv, rgdal

GDAL, R, mgcv, raster

C2, CALIB, Calib, R, clam

JAGS, R

BOLT-LMM, DISSECT, GTX, GenCall, HRC, IMPUTE, KING, METACARPA, METAL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, SNPTEST, ordinal

R, STATA

R, Stan, map2stan

R

R

Mice, R, Survival, lattice, mitml

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, Mice, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, lattice, mitml, samtools, survC1, survminer, tximport, xCell

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, tximport, xCell

Promasys, R, dplyr, psych

MATLAB

BLAST, Blastp, ClustalW, FastQC, IPA, MEGA, Mirdeep2, PRIMER, Primer-BLAST, R, SAS, SPSS, STAR, Samtools, TargetScan, Trimmomatic, edge, edgeR, gplots, miRDB

BOLT-LMM, DISSECT, GenCall, HRC, IMPUTE, KING, METACARPA, METAL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, SNPTEST, ordinal, rms

Matlab, R, adjustedRandIndex, lmer

FACSuite, Oligo Calc, Prism, cellSens Dimension

BD FACSDiva, BisoGenet, Cufflinks, Cytoscape, DAVID, FastQC, GSEA-P, Tophat, iGenomes

2LD, CLUMP, GENECOUNTING, GENEPOP, Haploview, MassARRAY Assay Design, MassARRAY Typer, windows

ArcGis, Maxent

ANNOVAR, BCFtools, BLAST, BWA-MEM, CNVmap, ConQuest, FACSuite, FastQC, FlexArray, GATK, GeneOverlap, Genomics Suite, ImagePro+, Mac OS X, Mirdeep2, MyIQ, Oligo Calc, PLINK, PLINK/SEQ, Partek, Picard, Plink, Primer-BLAST, Prism, R, RUMM, SAMtools, SPSS, STAR, STATA, Samtools, TargetScan, Trimmomatic, XHMM, bedtools, cellSens Dimension, cutadapt, eRM, edge, edgeR, gplots, ltm, miRDB, sickle, vegan

FreeSurfer, NeuroQuant, Quarc

AFNI, ANFI, DTIFit, FLIRT, FSL, FreeSurfer

MATLAB

BeadStudio, METAL, Mach, Mach2QTL, PLINK, SPSS Statistics

C++, OpenCL, R, glmnet

CloVR

ANNOVAR, BCFtools, BWA-MEM, GATK, GeneOverlap, PLINK, PLINK/SEQ, Picard, R, SAMtools, XHMM, bedtools, cutadapt, sickle

C, Linux, NovoSNP, Perl, SNPdetector, Unix

G*Power, Open Data Kit, R

CALIB, Calib, R, clam, rioja

CoNIFER, GATK, GEMINI, Genome Variation Server, MERLIN, MORGAN, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, SLINK, Seattle Seq, Variant Effect Predictor, cnvHap, mrsFAST

BEAGLE, CoNIFER, GATK, GEMINI, Genome Variation Server, MERLIN, MORGAN, PEDSTATS, PLINK, PennCNV, PolyPhen, SLINK, Seattle Seq, Variant Effect Predictor, cnvHap, mrsFAST

CubeX, DTIFit, FLIRT, FMRIB Software Library, FNIRT, FSL, FSL-VBM, MELODIC, SPSS, TBSS, VBM

CubeX, DTIFit, FLIRT, FMRIB Software Library, FNIRT, FSL, FSL-VBM, MELODIC, SPSS, TBSS, VBM, dual regression

CubeX, DTIFit, FLIRT, FMRIB Software Library, FNIRT, FSL, FSL-VBM, MELODIC, SPSS, Stata, TBSS, TrackVis, VBM, dual regression

CubeX, DTIFit, FLIRT, FMRIB Software Library, FNIRT, FSL, FSL-VBM, MELODIC, SPSS, TBSS, VBM, dual regression

CubeX, DTIFit, FLIRT, FMRIB Software Library, FNIRT, FSL, FSL-VBM, MELODIC, SPSS, TBSS, VBM, dual regression

AFNI, ANFI, CubeX, DTIFit, FMRIB Software Library, FNIRT, FSL, FSL-VBM, Fortran, FreeSurfer, MELODIC, SAMSCo, SPSS, TBSS, VBM, dual regression

CubeX, DTIFit, FLIRT, FMRIB Software Library, FSL, FSL-VBM, MELODIC, SPSS, TBSS, VBM, dual regression

CubeX, DTIFit, FLIRT, FMRIB Software Library, FNIRT, FSL, MELODIC, SPSS, TBSS, dual regression

Mricron, NeuroSynth, Nilearn, Python, SPM, Scikit-learn

CubeX, DTIFit, FLIRT, FMRIB Software Library, FNIRT, FSL, FSL-VBM, SPSS, TBSS, VBM, dual regression

CubeX, DTIFit, FLIRT, FMRIB Software Library, FNIRT, FSL, FSL-VBM, MELODIC, SPSS, TBSS, VBM, dual regression

CubeX, DTIFit, FLIRT, FMRIB Software Library, FNIRT, FSL, FSL-VBM, MELODIC, SPSS, VBM, dual regression

CLUMP, GENECOUNTING, GENEPOP, Haploview, MassARRAY Assay Design, MassARRAY Typer, PGA, windows

2LD, GENECOUNTING, GENEPOP, Haploview, MassARRAY Assay Design, MassARRAY Typer, PGA, windows

CADD, Condel, GATK, Geneious, ImageJ, Novoalign, Polyphen, Prism, Sift, VAX

Experiment Center, G*Power, iView X

BioConductor, Cluster, GSEA, Image-Pro Plus, J-Express, R, SAS, TreeView

Dataquest, Primer

3dClustsim, 3dDeconvolve, 3dDetrend, 3dFWHMx, 3dmaskave, 3dttest+ +, AFNI, Cogent, Matlab, SPSS, waver

AMBERTOOLS, Chimera, MOE, ORTEP, PASS, SADABS, SAINT, SHELXTL

C++, Linux, OpenSUSE, RHEL

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

Fiji, MATLAB, MorphoLibJ, Python

C++, Linux, Mac OS X, VirtualBox, Windows

BOLT-LMM, DISSECT, GTX, GenCall, HRC, IMPUTE, KING, METACARPA, METAL, PLINK, Quanto, R, SHAPEITv, SNPTEST, ordinal, rms

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

Java

R, dismo

AUTO, BioNetGen, CVODE, MatCont, RuleBender

C++, MinGW-w64, OSX, Windows, g++

C++, Linux, Perl, SSPACE-LongRead

Java, PathVisio

3dBandpass, 3dDespike, AFNI, BootES, Debian, FreeSurfer, MSM-All, MapIcosahedron, NeuroDebian, NeuroSynth, SUMA

AUTO, CVODE, MatCont, RuleBender, SUNDIALS

BEAST

GitHub, Java, JavaScript, MySQL, Tomcat

3dBandpass, 3dDespike, AFNI, BootES, Debian, FreeSurfer, MapIcosahedron, NeuroDebian, NeuroSynth, PyMVPA, SUMA

Matlab

ANNOVAR, BCFtools, BWA-MEM, C++, CNVmap, GATK, GeneOverlap, PLINK, PLINK/SEQ, Picard, R, SAMtools, XHMM, cutadapt, sickle

BEAGLE, CoNIFER, GATK, Genome Variation Server, MERLIN, MORGAN, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, SLINK, Seattle Seq, Variant Effect Predictor, cnvHap, mrsFAST

ANNOVAR, ASCAT, BCFtools, BWA-MEM, CNVmap, ChAMP, GATK, GeneOverlap, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, PLINK, PLINK/SEQ, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, SAMtools, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, XHMM, bam-readcount, bcl2fastq2, bedtools, consensus MIBC, cutadapt, edgeR, samtools, sickle, survival, survminer, tximport, xCell

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

R

GitHub, Python

GitHub, Ruby on Rails

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, edgeR, samtools, survival, survminer, tximport, xCell

BD FACSDiva, BisoGenet, Cytoscape, DAVID, FastQC, GSEA-P, Tophat, iGenomes

Google Earth, MaxEnt, SDMtoolbox

C, C++, Objective-C, OsiriX, REMIT, ReMIT, ReMIT Client, ReMITclient, dcm4che

ARLEQUIN, Arlequin, BEAST, BIOEDIT, BLAST, Bioportal, Bottleneck, CLUMPP, Clustal W, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FREENA, FSTAT, Fig Tree, Fstat, GENELAND, GENEMAPPER, GENEPOP, GenePop, Geneland, Google Earth, IBDWS, LAGRANGE, LogCombiner, MEGA, MICRO-CHECKER, MRBAYES, MrBayes, NETWORK, Network, PAUP, PAUP*, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, Structure, TRACER, Tracer, TreeAnnotator, VIP, beast, convert, genemapper, migrate

ASCAT, ChAMP, GATK, GenomeStudio, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

MDAnalysis, Python

Biopython, Python, Reportlab, matplotlib

Java

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

FigureJ, ImageJ, Immunoratio, Java, R, ROCR

R, ggplot2

H2O R interface, R, Windows, pROC

Python

BOLT-LMM, DISSECT, GTX, GenCall, HRC, IMPUTE, KING, METAL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, SNPTEST, ordinal, rms

BWA, DESeq, FIMO, GOseq, KOBAS, MACS, Perl, R, TopHat, skewer

CellProfiler, Fiji, MATLAB, Python

BioPython, HMMER, IDEPI, Python, VirtualBox, scikit-learn

Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RNA-Skim, RSeQC, RTA, Rtsne, STAR, Subread, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

Linux, Mac, Windows

ANNOVAR, BCFtools, CNVmap, DESeq, FIMO, GATK, GOseq, GeneOverlap, HTSeq, KOBAS, MACS, PLINK, PLINK/SEQ, Perl, Picard, R, SAMtools, TopHat, XHMM, bedtools, cutadapt, sickle, skewer

ANNOVAR, BCFtools, BWA-MEM, CNVmap, GATK, GeneOverlap, PLINK, PLINK/SEQ, Picard, R, SAMtools, XHMM, bedtools, sickle

Java

GitHub

Linux, MacOS, Python

CADD, Condel, GATK, Geneious, Genome Analysis Toolkit, ImageJ, Novoalign, Polyphen, Prism, Sift

ANNOVAR, BCFtools, BWA-MEM, CNVmap, GATK, GeneOverlap, PLINK, PLINK/SEQ, Picard, R, SAMtools, XHMM, bedtools, cutadapt

CLC Genomic Workbench, GARLI, Newbler, Novoalign, Python, SAMtools, SMRT analysis, github

COBRAme, Python

MATLAB

GitHub, Java, Javascript

BLAST, FastQC, IPA, Primer-BLAST, R, SPSS, STAR, Samtools, TargetScan, Trimmomatic, edge, edgeR, gplots, miRDB, vegan

Arlequin, BLAST, Bottleneck, Clustal W, DnaSP, EXCEL, Fstat, GenePop, Geneland, Google Earth, IBDWS, LogCombiner, MEGA, Modeltest, MrBayes, Network, PAUP*, Structure, Tracer, TreeAnnotator, beast, convert, genemapper, migrate

ARLEQUIN, BEAST, BIOEDIT, Bioportal, CLUMPP, DISTRUCT, DIYABC, Datamonkey, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, LAGRANGE, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, NETWORK, PAUP, PHASE, PhyML, SPLITSTREE, STRUCTURE, TRACER, VIP

R, Rstan, Stan

Matlab

C++

ANNOVAR, BWA-MEM, CNVmap, GATK, GeneOverlap, PLINK, PLINK/SEQ, Picard, R, SAMtools, XHMM, bedtools, cutadapt, sickle

BLASTp, BioTools, FGENESB, Flex Analysis, InterPro, MASCOT, PhylopythiaS, ProteomeWeaver, SigmaPlot, SigmaStat

COBRApy, Python

Brain Vision Recorder, Excel, MATLAB, MapWin, Mapwin, Matlab, SPSS, Stan, WinEEG, sLORETA

GitHub, OpenCV, Python, Qt

HGF, Matlab, Psychophysics Toolbox, SPM, SPSS, Windows

AUTO, BioNetGen, MatCont, RuleBender, SUNDIALS

BLAST, Bowtie, FastQC, IPA, Mirdeep2, Primer-BLAST, R, SPSS, STAR, Samtools, TargetScan, edge, edgeR, gplots, miRDB, vegan

ARLEQUIN, BEAST, BIOEDIT, BLAST, BioMart, Biomart, Bioportal, CLUMPP, ClustalW, DISTRUCT, DIYABC, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, Geneious, HyPhy, LAGRANGE, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, MrBayes, NETWORK, PAUP, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, TRACER, VIP

BioPython, HMMER, Python, VirtualBox, joblib, scikit-learn

GitHub, Linux, MacOS X, Pathomx, Python, Qt, Ubuntu, Windows

github

BEAGLE, CoNIFER, GATK, GEMINI, MERLIN, MORGAN, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, SLINK, Seattle Seq, Variant Effect Predictor, cnvHap, mrsFAST

BOLT-LMM, DISSECT, GTX, GenCall, HRC, IMPUTE, KING, METACARPA, METAL, PLINK, R, SHAPEITv, SMARTPCA, SNPTEST, ordinal, rms

Excel, Stata

Stata

STATA

Axio Vision, CAD, CFD, Fiji, GraphPad, Illustrator, ImageJ, LAS X, Photoshop, Prism, Quicktime

BioConductor, Cluster, GSEA, Image-Pro Plus, LAS, R, SAS, TreeView

Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RSeQC, Rtsne, STAR, Sailfish, Subread, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, Genepix Pro, Prism, R, RSeQC, RTA, Rtsne, STAR, Sailfish, Subread, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

2LD, ARLEQUIN, Arlequin, BEAST, BIOEDIT, BLAST, BOTTLENECK, Bioportal, Bottleneck, CLUMP, CLUMPP, COANCESTRY, COLONY, Clustal W, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FREENA, FSTAT, Fig Tree, Fstat, GENECOUNTING, GENELAND, GENEMAPPER, GenAlEx, Geneland, Genescan, Google Earth, Haploview, IBDWS, LAGRANGE, LogCombiner, MEGA, MICRO-CHECKER, MICROCHECKER, MLRELATE, MODELTEST, MRBAYES, MassARRAY Assay Design, MassARRAY Typer, Modeltest, MrBayes, NETWORK, Network, PAUP, PAUP*, PGA, PHASE, Peakscanner, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, Structure, TRACER, Tracer, TreeAnnotator, VIP, beast, convert, genemapper, migrate, windows

BOLT-LMM, DISSECT, GTX, GenCall, HRC, IMPUTE, KING, METACARPA, METAL, PLINK, Quanto, R, SMARTPCA, SNPTEST, ordinal, rms

BOLT-LMM, DISSECT, GTX, GenCall, HRC, IMPUTE, KING, METACARPA, METAL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, ordinal, rms

BOLT-LMM, DISSECT, GTX, GenCall, HRC, KING, METACARPA, METAL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, SNPTEST, ordinal, rms

MATLAB, Photoshop

Image Processing Toolbox, Matlab

E-prime, Linux, MATLAB, MacOSX, Matlab, Mindboggle, Windows

Goldwave, Matlab

EEGLab, Excel, MATLAB, MapWin, Mapwin, SPSS, sLORETA

DS modeling, ENSEMBLE, Igor pro, Photoshop, VideoTrack, Videotrack, Visilog

3dBandpass, 3dDespike, AFNI, BootES, Debian, FreeSurfer, MSM-All, MapIcosahedron, NeuroSynth, PyMVPA, SUMA

AlphaSim, REST, SPM, SPSS Statistics, Talairach Daemon, WFU pickatlas

BOLT-LMM, DISSECT, GTX, GenCall, HRC, IMPUTE, METACARPA, METAL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, SNPTEST, ordinal, rms

3dFDR, AFNI, EyeLink Data Viewer, Matlab, Python, SPSS

Arlequin, BLAST, Bottleneck, Clustal W, DnaSP, EXCEL, Fig Tree, Fstat, GenePop, Geneland, Google Earth, IBDWS, LogCombiner, MEGA, Modeltest, MrBayes, Network, PAUP*, Structure, Tracer, TreeAnnotator, beast, convert, genemapper

Artemis, BLASTp, BioTools, FGENESB, Flex Analysis, InterPro, MASCOT, ProteomeWeaver, SigmaPlot, SigmaStat

ArcGIS, ENVI, Fragstats, STATA

ImageJ, Patchmaster, Prism, Videomot

Brain Vision Analyzer, Experimetrix, GoldWave, MATLAB, Marsbar, SPM, SPSS, image processing toolbox

FSLView, Mricron, NeuroSynth, Python, SPM, Scikit-learn

MATLAB

Netcdf, NumPy, PyMS, Pycluster, Python, matplotlib, tcl, tk

GSEA, TensorFlow, caret, irr, mRMRe, survcomp

Artemis, BLASTp, BioTools, FGENESB, Flex Analysis, InterPro, MASCOT, PhylopythiaS, ProteomeWeaver, SigmaPlot, SigmaStat

ProctorU, R, ggplot2

ARLEQUIN, BEAST, BIOEDIT, Bioportal, DISTRUCT, DIYABC, Datamonkey, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, LAGRANGE, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, NETWORK, PAUP, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, TRACER, VIP

ARLEQUIN, BEAST, BIOEDIT, Bioportal, CLUMPP, DIYABC, Datamonkey, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, LAGRANGE, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, NETWORK, PAUP, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, TRACER, VIP

C++

BLASTp, Bioplex Manager, Epi, MSstats, R, Skyline

CADD, Condel, GATK, Geneious, Genome Analysis Toolkit, ImageJ, Novoalign, Polyphen, Prism, VAX

STATA, Windows Mobile

MATLAB, Matlab, Mixer, R, adjustedRandIndex, lmer

C++

Arlequin, Network, STATISTICA, SeqScape

Matlab

BEAGLE, CoNIFER, GATK, GEMINI, Genome Variation Server, MERLIN, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, SLINK, Seattle Seq, Variant Effect Predictor, cnvHap, mrsFAST

BEAGLE, CoNIFER, GATK, GEMINI, Genome Variation Server, MERLIN, MORGAN, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, SLINK, Variant Effect Predictor, cnvHap, mrsFAST

BLAST, Genome browser, PLINK, PolyPhen, Primer

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

Linux, Perl, R

Arlequin, BLAST, Bottleneck, Clustal W, DnaSP, EXCEL, Fig Tree, Fstat, GenePop, Geneland, Google Earth, LogCombiner, MEGA, Modeltest, MrBayes, Network, PAUP*, Structure, Tracer, TreeAnnotator, beast, convert, genemapper, migrate

ImageJ, Windows

AUTO, BioNetGen, CVODE, RuleBender, SUNDIALS

BWA, DESeq, FIMO, GOseq, HTSeq, KOBAS, MACS, Perl, R, TopHat

ANNOVAR, BCFtools, BWA-MEM, CNVmap, GATK, GeneOverlap, PLINK, PLINK/SEQ, Picard, R, SAMtools, bedtools, cutadapt, sickle

Pong

BD FACSDiva, BisoGenet, Cufflinks, Cytoscape, DAVID, FastQC, GSEA-P, Tophat

BEAST, GitHub

R, SOCPROG, boot

Alogps, MultiPak

BOTTLENECK, COANCESTRY, COLONY, GENEPOP, GenAlEx, MICROCHECKER, MLRELATE, Peakscanner

Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RSeQC, RTA, Rtsne, STAR, Sailfish, Subread, TreeView, Treeview, immunoSEQ Analyzer

Stata

AFNI, ANFI, CubeX, FLIRT, FMRIB Software Library, FNIRT, FSL, FSL-VBM, FreeSurfer, MELODIC, SAMSCo, SPSS, TBSS, VBM, dual regression

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

Habit 2000, TouchStat

ADMIXMAP, ARLEQUIN, Arlequin, BEAST, BIOEDIT, BLAST, Bioportal, Bottleneck, CLUMPP, Clustal W, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FREENA, FSTAT, Fig Tree, Fstat, GENELAND, GENEMAPPER, GENEPOP, GenePop, Geneland, Google Earth, IBDWS, LAGRANGE, LogCombiner, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, Modeltest, MrBayes, NETWORK, Network, PAUP, PAUP*, PHASE, PhyML, SPAGeDI, SPLITSTREE, TRACER, Tracer, TreeAnnotator, VIP, beast, convert, genemapper, migrate

Autodock Vina, CellQuest, CompuSin, CompuSyn, Linux Red Hat, Prism, PyMOL, Quantity One, Vina

Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RSeQC, RTA, Rtsne, STAR, Sailfish, Subread, ToppFun, TreeView, Treeview

CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RSeQC, RTA, Rtsne, STAR, Sailfish, Subread, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

Prism

MassHunter Acquisition, Prism

MassHunter Acquisition, Prism

Firefox, SPSS

STATA

CAD, Fiji, Illustrator, Imaris, LAS X, Photoshop, Prism, Quicktime

MEGA, Mothur, Venny

Inxight, NLTK, Python, Yahoo-BOSS, Yahoo-BOSS API

BisoGenet, Cufflinks, Cytoscape, DAVID, FastQC, GSEA-P, Tophat, iGenomes

Oligo Calc, Prism, cellSens Dimension

Arlequin, BLAST, Bottleneck, Clustal W, DnaSP, EXCEL, Fig Tree, Fstat, GenePop, Geneland, Google Earth, IBDWS, LogCombiner, MEGA, Modeltest, MrBayes, Network, PAUP*, Structure, Tracer, beast, convert, genemapper, migrate

Iox, Kubios, Kubios HRV, MCODE, ModFit, PPI Network, Prism, SPSS, TargetScan, Venny, Xena, miRDB, microRNA

FlexArray, ImagePro+, STATA

AMIX, Autodock Vina, CellQuest, Chenomx, Chenomx NMR Suite, CompuSin, CompuSyn, Cytobank, Fiji, ImageJ, InsightII, Linux Red Hat, Metamorph, Prism, PyMOL, Rotor-Gene Q, SIMCA-P, SPSS, TANRIC, TopSpin, Vina

Analyst, BLASTp, Epi, MSstats, R, Skyline

Artemis, BLASTp, BioTools, FGENESB, Flex Analysis, InterPro, MASCOT, PhylopythiaS, SigmaPlot, SigmaStat

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

BLAST, FastQC, IPA, Mirdeep2, Primer-BLAST, R, SPSS, STAR, Samtools, TargetScan, Trimmomatic, edgeR, gplots, miRDB, vegan

GSEA, PyRadiomics, TensorFlow, caret, irr, mRMRe

AccuTyping, GenePix

SPSS

EEGlab

E-Prime, Experimetrix, FMRIB Software Library, FSL

MACH, PLINK

AMIX, Chenomx, Chenomx NMR Suite, Cytobank, Fiji, ImageJ, Prism, Quantity One, Rotor-Gene Q, SIMCA-P

Artemis, BLASTp, BioTools, FGENESB, InterPro, MASCOT, PhylopythiaS, ProteomeWeaver, SigmaPlot, SigmaStat

Chenomx, Chenomx NMR Suite, Cytobank, Fiji, ImageJ, Prism, Quantity One, Rotor-Gene Q, SIMCA-P, TopSpin

AMBERTOOLS, CPPTRAJ, Chimera, CrystalClear, MOE, PASS, PLATON, SADABS, SAINT, SHELXL, SHELXS, SHELXTL, Windows

AMIX, Cytobank, Fiji, ImageJ, Prism, Quantity One, Rotor-Gene Q, SIMCA-P, TopSpin

Mechanical Turk, PRAAT

Autodock Vina, CellQuest, Excel, InsightII, Linux Red Hat, Prism, PyMOL, Quantity One, Vina

FreeSurfer, Quarc

ImageJ, NIS-Elements, Qbase+, prism

GeNorm, Primer

C, C++, Objective-C, OsiriX, REMIT, ReMIT, ReMIT Client, ReMITclient, dcm4chee

Image Lab, Kubios, Kubios HRV, Prism

BEAGLE, CoNIFER, GATK, GEMINI, Genome Variation Server, MERLIN, MORGAN, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, SLINK, Seattle Seq, cnvHap, mrsFAST

Brain Vision Analyzer, E-Prime

Igor pro, Photoshop, VideoTrack, Videotrack, pClamp

MATLAB, SPM

ARLEQUIN, Arlequin, Arlequín, BEAST, BIOEDIT, BLAST, BioEdit, Bioportal, Bottleneck, CLUMPP, Clustal W, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FREENA, FSTAT, Fig Tree, Fstat, GENELAND, GENEMAPPER, GENEPOP, GenePop, Geneland, Google Earth, IBDWS, LAGRANGE, LogCombiner, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, Modeltest, MrBayes, PAUP, PAUP*, PHASE, PhyML, SPAGeDI, SPLITSTREE, SPSS, STATISTICA, STRUCTURE, SeqScape, Sequence Scanner, Structure, Surfer, TRACER, Tracer, TreeAnnotator, VIP, beast, convert, genemapper, migrate, mtPhyl

IVICT, MATLAB, Praat

ICC toolbox, LI-toolbox, MATLAB, Macintosh, Presentation, SPM, SPSS, SPSS Statistics, WFU-Pickatlas

Matlab

BD FACSDiva, BioConductor, BisoGenet, Cluster, Cufflinks, Cytoscape, DAVID, FastQC, Image-Pro Plus, J-Express, LAS, PyRadiomics, R, SAS, TensorFlow, Tophat, TreeView, caret, iGenomes, irr, mRMRe, survcomp

Pajek, R, bipartite, netcarto

MLwiN, SAS

ImageJ, Prism, Spectrum Mill, Videomot

BLAST, BioMart, Biomart, ClustalW, Datamonkey, Geneious, MEGA, MrBayes

SPSS Statistics

SPSS

SPSS, SPSS Statistics, Windows

Crimap, QTL Express, R/Qtl

GRIMP, METAL, Mach, Mach2QTL, PLINK, SPSS Statistics

BOLT-LMM, DISSECT, GTX, HRC, IMPUTE, KING, METACARPA, METAL, PLINK, Quanto, R, SHAPEITv, SMARTPCA, SNPTEST, ordinal, rms

ASCAT, BLAST, ChAMP, GATK, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

PhyloGibbs-MP

PhyloGibbs

DCE@urLAB, IDL Virtual Machine, Windows

DCE@urLAB, IDL, Windows

BEAGLE, CoNIFER, GATK, GEMINI, Genome Variation Server, MERLIN, MORGAN, PBAP, PEDSTATS, PLINK, PennCNV, PolyPhen, Seattle Seq, Variant Effect Predictor, cnvHap, mrsFAST

Digilab, SPSS

Image Lab, Iox, MATLAB, Prism

ArcGIS, Fragstats, STATA, Spatial Statistics

Arlequin, Arlequín, BioEdit, Network, SPSS, Surfer

CAD, CFD, Fiji, Illustrator, Imaris, Photoshop, Prism, Quicktime

SPSS, Windows

excel

Excel, Illustrator, Office, Prism, SPSS Statistics

BioConductor, Cluster, FlexArray, GSEA, J-Express, LAS, MyIQ, Office Excel, Photoshop, R, SAS, STATA, Satistix, Scope-Pro, SigmaPlot, SigmaStat, TreeView, Windows

ICC toolbox, MATLAB, Macintosh, Presentation, SPM, SPM anatomy toolbox, SPSS, SPSS Statistics, WFU-Pickatlas

SAS

Statistica

HVS Image, Image J, ImageJ, ImageQuant TL, Qbase+, SPSS, prism

C#, Java, Matlab, Python, R, Visual Studio, Windows

Stata

Ledalab, MATLAB, Psychtoolbox

EEGLab, Excel, MATLAB, MapWin, Mapwin, SPSS, WinEEG

AccuTyping, Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, FlowJo, Gene Cluster, ImaGene, PIVOT, Prism, R, RSeQC, RTA, Rtsne, STAR, Sailfish, Subread, ToppFun, TreeView, Treeview, immunoSEQ Analyzer

DTV.II SR, Primer, Quantity One, SPSS, Virtuoso, Volume 1

BOTTLENECK, COANCESTRY, COLONY, GENEPOP, GenAlEx, Genescan, MICROCHECKER, Peakscanner

JWatcher, SPSS

FragIt

BLAST, FastQC, IPA, Mirdeep2, R, SPSS, STAR, Samtools, TargetScan, Trimmomatic, edge, edgeR, gplots, miRDB, vegan

BrainVoyager, ICC toolbox, LI-toolbox, MATLAB, Macintosh, MarsBar, PASW Statistics, SPM, SPM anatomy toolbox, SPSS, SPSS Statistics, WFU-Pickatlas, WFU-pick atlas

CONN, FSL, SPM, conn

AFNI, FSL, MATLAB, Psychophysics Toolbox, SPM, ViewPoint

BeadStudio, GRIMP, METAL, Mach, PLINK, SPSS Statistics

FSLView, NeuroSynth, Nilearn, Python, SPM, Scikit-learn

MATLAB

ART, CONN, DARTEL, FSL, ICC toolbox, LI-toolbox, MATLAB, Macintosh, MarsBar, Marsbar, Presentation, SPM, SPM anatomy toolbox, SPSS, SPSS Statistics, Talairach Daemon, conn

ARLEQUIN, Arlequin, Arlequín, BEAST, Bioportal, CLUMPP, DISTRUCT, DIYABC, Datamonkey, EpiR, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, LAGRANGE, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, NETWORK, Network, PAUP, PHASE, PhyML, QGIS, R, SPAGeDI, SPLITSTREE, SPSS, STRUCTURE, Sequence Scanner, Surfer, TRACER, VIP, ggplot2, mgcv

FACSuite, Oligo Calc, Prism

CLC Genomic Workbench, GARLI, Newbler, Novoalign, Python, SAMtools, github

Ingenuity, Mac OS X, Prism

Gower, SPSS

Bootstrap, SPSS

R, dplyr, psych, tidyr

Alogps, iTeva

CrystalClear, ORTEP, SHELXL, SHELXS, Windows

SPSS

R, Remote Proctor Now, ggplot2

Bioworks, ClueGO, Cytoscape, FunRich, MASCOT, Office Excel, Prism, Reactome, clusterMaker, cytoscape

Genevestigator, ImageJ, ImageQuant TL, NIS-Elements, Statistica, prism

AMIX, Chenomx, Chenomx NMR Suite, Cytobank, Fiji, ImageJ, Prism, Quantity One, SIMCA-P, TopSpin

FreeSurfer, NeuroQuant

SAS, SPSS

ORTEP, PLATON, SHELXL, SHELXS, Windows

Eyelink Toolbox, Matlab, Psychtoolbox

AMIX, Chenomx, Chenomx NMR Suite, Cytobank, Fiji, ImageJ, Prism, Quantity One, Rotor-Gene Q, TopSpin

CFD, Fiji, Illustrator, Imaris, LAS X, Photoshop, Prism, Quicktime

3dFDR, AFNI, Matlab, Python, SPSS, iMap

Matlab, R

SPSS Statistics

IPP, Image-Pro Plus, Office Excel, Photoshop, Scope-Pro, SigmaPlot, SigmaStat, Windows

AmeliaView, SPSS, SPSS Statistics, Stata, Windows

GraphPad, MATLAB, NeuroExplorer

GraphPad, MATLAB, NeuroExplorer, Open sorter

Matlab

ArcGIS

Image lab, MCODE, ModFit, SPSS, TargetScan, Venny, Xena, miRDB, microRNA

BOTTLENECK, COANCESTRY, COLONY, GENEPOP, GenAlEx, Genescan, MICROCHECKER, MLRELATE

Arlequin, Network, STATISTICA, mtPhyl

LSM imaging, Openlab

OriginLab

ImageJ, Patchmaster, Prism, Spectrum Mill

SAS

R, mice

BioPython, FSLView, HMMER, IDEPI, Mricron, NeuroSynth, Nilearn, Python, SPM, VirtualBox, joblib

Promasys, R, psych, tidyr

MapInfo Professional, R, SAS, SPSS, Stata, Windows

Excel

ARLEQUIN, Arlequin, BEAST, BIOEDIT, BLAST, BioMart, Biomart, Bioportal, Bottleneck, CLUMPP, Clustal W, ClustalW, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FREENA, FSTAT, Fig Tree, Fstat, GENELAND, GENEMAPPER, GENEPOP, GenePop, Geneious, Geneland, Google Earth, HyPhy, IBDWS, LAGRANGE, LogCombiner, MEGA, MICRO-CHECKER, MODELTEST, Modeltest, NETWORK, Network, PAUP, PAUP*, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, Structure, TRACER, Tracer, TreeAnnotator, VIP, beast, convert, genemapper, migrate

BLAST, Blast, DTV.II SR, Dataquest, Ensembl, GeNorm, Genome browser, Image J, MetaMorph, Mutation Surveyor, OptimalCutpoints, PLINK, PolyPhen, Q-LAB, R, SAS, SPSS, Vegan, Virtuoso, Volume 1

Excel, Illustrator, Med-PC, MedPC, NVivo, Prism, SPSS Statistics, Word

Excel, MSOffice, NVivo

EASY RA1 Easy Randomizer, Excel, SAS

Access, ActiLife, ArcView, Arlequin, BLAST, BiNGO, Bioworks, Bottleneck, ClueGO, Clustal W, CompuSyn, Cytoscape, DIVA-GIS, Datacam, DnaSP, EASY RA1 Easy Randomizer, EEGLab, EPI INFO, EQ-5D calculator, Fig Tree, Fstat, FunRich, GenePop, Geneland, Globalpark, Google Earth, IBDWS, IPP, Illustrator, Image J, Image-Pro Plus, LogCombiner, MASCOT, MATLAB, MEGA, MSOffice, Mac, MapWin, Mapwin, Med-PC, MedPC, Modeltest, MrBayes, NVivo, Network, Office, OriginPro, PAUP*, PRISM, Photoshop, PowerPoint, Prism, QGIS, R, Reactome, Refworks, SAS, SNAP, SPSS, SPSS Dimensions, SPSS Statistics, STATA, Satistix, Scope-Pro, SigmaPlot, SigmaStat, Stata, Stereo investigator, Structure, SurveyMonkey, Tableau, Tracer, TreeAnnotator, Unix, VBA, WinEEG, Windows, Word, XLSTAT, beast, clusterMaker, convert, cytoscape, genemapper, metareg, migrate, sLORETA

ImageJ, Java, LAMINA

C, Excel, Java, Linux, NemaFootPrinter, NovoSNP, Perl, PolyPhred, SNPdetector, SQL

BioPython, C++, Chaste, Chrome, Django, Firefox, HMMER, HTML, IDEPI, Internet Explorer, Linux, Mac OS X, PhosphOrtholog, Python, R, Safari, Windows, jQuery, joblib, scikit-learn

ArcView, Excel, QGIS, SPSS Statistics

FDT, FSL, Stata, TrackVis

ImageJ, R, SAS, SPSS, nlme

ArcGIS, CANTAB, CT-Expo, Chart, ENVI, EPI Info, Epi Info, EpiData, EpiData Analysis, EpiInfo, Epidata, Excel, FDT, FSL, FlexArray, Fragstats, GPS Sample, ICE, ImagePro+, Inquisit, MLWiN, MLwiN, Macintosh, Microsoft Office Excel, Mplus, MyIQ, NQuery Advisor, Newborn Size Application, QGIS, R, R Studio, REALCOM-IMPUTE, RIU, RevMan, Review Manager, SAS, SPSS, SQL, Spatial Statistics, Statistica, TrackVis, Windows, Windows Mobile, ZSCORE06, excel, glmnet, ice, metareg, punafcc, rpart, runmlwin, traj

ArcGIS, EstimateS, R, lme4

CAD, CFD, Fiji, Illustrator, Imaris, LAS X, Photoshop, Prism

Epi Info, SAS

CAD, CFD, Curve Fitting Toolbox, Fiji, IPP, Igor pro, Illustrator, Image-Pro Plus, Imaris, LAS X, MATLAB, Office Excel, Pixelmator, Prism, Quicktime, R, Satistix, Scope-Pro, SigmaPlot, SigmaStat, VideoTrack, Videotrack, Visilog, Visual Basic, Windows, lme4, pClamp

C, C++, Objective-C, REMIT, ReMIT, ReMIT Client, ReMITclient, dcm4che, dcm4chee

Excel, Xcalibur

ArcView, BioEdit, DIVA-GIS, EpiR, Excel, MEGA, R, SPSS Statistics, STATA, ggplot2, mgcv

Sente

C#, Java, Matlab, NET, Python, R, Windows

AMIX, Autodock Vina, Axio Vision, BiNGO, Bioanalyzer, Bioworks, CAD, CADD, CASAVA, CFD, CIBERSORT, CellQuest, Chenomx, Chenomx NMR Suite, ClueGO, Cluster, CompuSin, CompuSyn, Condel, Cytobank, Cytoscape, DESeq2, EdgeR, Excel, FACSuite, Fiji, FlowJo, FunRich, G*Power, GATK, Gene Cluster, Geneious, Genepix Pro, Genome Analysis Toolkit, Genomics Suite, IMARIS, Illustrator, Image J, Image Lab, Image-J, ImageJ, ImageQuant TL, Imaris, Ingenuity, InsightII, Instat, Iox, Kubios, Kubios HRV, LAS X, Linux Red Hat, MASCOT, MATLAB, MEGA, MUSCLE, Mac OS, Mac OS X, MacOS, MassHunter Acquisition, Med-PC, MedPC, NIS-Elements, NeuroExplorer, Novoalign, Office, Office Excel, Oligo Calc, Open sorter, PIVOT, Partek, Patchmaster, Photoshop, Polyphen, PyMOL, Qbase+, Quantity One, Quicktime, R, RSeQC, RTA, Reactome, Rotor-Gene Q, Rtsne, SIMCA-P, SPSS, SPSS Statistics, STAR, Sailfish, Sift, Spectrum Mill, Statistica, Subread, TANRIC, TopSpin, ToppFun, TreeView, Treeview, VAX, Videomot, Vina, Windows, ZEN, cellSens Dimension, clusterMaker, cytoscape, immunoSEQ Analyzer, windows

Photoshop, VideoTrack, Videotrack, Visilog, pClamp

Autodock Vina, CellQuest, CompuSin, CompuSyn, InsightII, Linux Red Hat, Prism, Quantity One, Vina

2LD, ACME, Access, AmeliaView, ArcGIS, C, C#, C++, CLUMP, Chaste, CoXpress, CrystalClear, DCE@urLAB, DelPhi, EPI info, EpiInfo, Excel, FIMTrack, Fortran, GENECOUNTING, GENEPOP, GenomePop, GraphPad, H2O R interface, HGF, Haploview, IDL, IDL Virtual Machine, IHC Profiler, IHC profiler, IPP, Image J, Image Processing Toolbox, Image-Pro Plus, ImageJ, Imagelab, JAVA, Java, Java Runtime Environment, Java Virtual Machine, LISREL, Linux, Luminex 100 ™ IS, MIiSR, MPlus, Mac, Mac OS X, MacOS X, MacOSX, Macintosh, MassARRAY Assay Design, MassARRAY Typer, Matlab, MetaSel, MicroSyn, MinGW-w64, Mindboggle, Mplus, NET, ORTEP, OSX, Office Excel, PASW, PASW Statistics, PGA, PLATON, Pathomx, Pep2Path, Photoshop, PhysiCell, Prism, ProteoLens, Psychophysics Toolbox, PyPi, Python, Qt, QuickPALM, R, RevMan, SAS, SHELXL, SHELXS, SPM, SPSS, SPSS Amos, SPSS Statistics, SPSS statistics, STATA, STATISTICA, Satistix, Scope-Pro, Sigma plot, SigmaPlot, SigmaStat, Stata, Statistica, TAPAS, Ubuntu, VirtualBox, Visual Basic, Visual Studio, WPS, WholePathwayScope, biographer, cellXpress, coXpress, g++, gdata, gplots, gtools, h2oEnsemble, hgu95av2, hu6800, linux, pROC, plotrix

ACME, C, C++, CBFA, Chaste, Datacam, DelPhi, Excel, FIMTrack, Fortran, GLPK, GenomePop, Genomics Suite, ICC toolbox, Image Processing Toolbox, ImageJ, Ingenuity, JDK, Java, Java JRE, LI-toolbox, Linux, MATLAB, MIiSR, Matlab, MinGW-w64, Mindboggle, NLME, OptFlux, Optflux, Partek, Pathomx, Pep2Path, PhysiCell, Presentation, Prism, Psychophysics Toolbox, PyPi, Python, Qt, QuickPALM, R, R Studio, SPM, SPM anatomy toolbox, SPSS, SPSS Statistics, STATA, Telescope, Ubuntu, VirtualBox, WFU-Pickatlas, Windows, g++

CBFA, GLPK, JAVA, JDK, Java, Java Virtual Machine, Mac OS, OptFlux, Optflux, ProteoLens, Windows

Chrome, Django, Firefox, HTML, PhosphOrtholog, Python, R, Safari, VirtualBox, jQuery

C#, C++, DelPhi, Fortran, Linux, Mac, NovoSNP, Objective-C, OsiriX, PEPIS, PERL, Perl, PolyPhred, PoreWalker, REMIT, ReMIT, ReMIT Client, ReMITclient, SNPdetector, Unix, VASP-E, Visual Basic, Windows, dcm4che, dcm4chee, gcc, linux

Attivio, Inxight, Python, Yahoo-BOSS, Yahoo-BOSS API

GitHub, M-Track, Python, Qt

Actionscript, MacVide, Matlab

AMIX, Axio Vision, CADD, Chenomx, Chenomx NMR Suite, Condel, Cytobank, Ensembl, Excel, FigureJ, Fiji, GATK, Geneious, Genome Analysis Toolkit, GraphPad, HVS Image, IHC Profiler, IHC profiler, IMARIS, ImageQuant TL, Immunoratio, Instat, JMP, Java, Java Advanced Imaging, Ki67 Vv, LAMINA, MacOS, NIS, NIS-Elements, Novoalign, Patchmaster, Polyphen, Primer3 Input, Prism, Q-LAB, Qbase+, Quantity One, R, ROCR, Rotor-Gene Q, SIMCA-P, SPSS, Sift, Spectrum Mill, Statistica, TopSpin, VAX, Videomot, Windows, nlme, prism

C++, Linux, NFTsim, RHEL

3dClustsim, 3dDeconvolve, 3dDetrend, 3dFDR, 3dFWHMx, 3dmaskave, 3dttest+ +, ADAPT, AFNI, Actionscript, Anatomy atlas, AsReml, BVQX, Behavior Annotator, Biotrace, BrainStorm, BrainVoyager, Brainsight, C#, CGBayesNets, CellProfiler, Cogent, Cogent 2000, Ctrax, Curve Fitting Toolbox, E-prime, EEGLAB, EEGLab, Excel, Experiment Builder, EyeLink API, EyeLink Data Viewer, Eyelink Toolbox, FSL, Fieldmap, Fiji, FixErrors, Flash, Gannet, GitHub, Goldwave, Google Cloud, GraphPad, HGF, ICC toolbox, ISC-toolbox, IVICT, Image Processing Toolbox, Java, Kubios HRV, LAN toolbox, LI-toolbox, LabVIEW, Ledalab, Linux, MIiSR, MacOSX, MacVide, Macintosh, MapWin, Mapwin, Metabomatching, Mindboggle, Mixer, MorphoLibJ, NET, NIRS_SPM, NeuroExplorer, NeuroMap, NumPy, OS-X, Open sorter, PASW Statistics, PRTools, PSAMM, Photoshop, Praat, Presentation, Psychophysics Toolbox, Psychophysics toolbox, Psychtoolbox, Python, QuickPALM, R, REGRESSIONv2.m, SPIKE-dist, SPM, SPM anatomy toolbox, SPSS, SPSS Statistics, Scan, SciPy, ScopeWin, Statistical Toolbox, TAPAS, Techila Technologies, Tensor Toolbox, ViewPoint, Visual C++, Visual Studio, WFU-Pickatlas, WinEEG, Windows, adjustedRandIndex, articulatory synthesizer, get_totals, iMap, image processing toolbox, lmer, neurofeedback toolbox, openMEEG, sLORETA, statistics toolbox, tnet, voicebox, waver

Java, PathVisioRPC

BLAST, ClustalW, GlobalWorks, MASCOT, Muscle, PhyML, SMART, SPSS, SignalP

SPSS, WinEpiscope

Matlab, Techila Technologies

EEGLAB, R, Rstan, map2stan

Artemis, BLAST, BLASTp, BiNGO, BioTools, Bioworks, ClueGO, ClustalW, Cytoscape, FGENESB, Flex Analysis, FunRich, GlobalWorks, I-TASSER, InterPro, Muscle, Office Excel, PhyML, PhylopythiaS, Prism, ProteomeWeaver, Reactome, SMART, SPSS, SigmaPlot, SigmaStat, SignalP, clusterMaker, cytoscape

Arlequin, Genevestigator, Image-J, Network, Prism, R, SeqScape, Sperm Class Analyzer, Stata, Windows, glmnet, mtPhyl, qBase

C, C++, MinGW-w64, OSX, PhysiCell, VASP-E, Windows, linux

GDAL, R, mgcv, raster, rgdal

2LD, 3dClustsim, 3dDeconvolve, 3dDetrend, 3dFDR, 3dFWHMx, 3dmaskave, 3dttest+ +, AFNI, AMOS, ATLAS.ti, Access, AcqKnowledge, ActiLife, Advanced Model, Altmetric, ArcView, Arlequin, Arlequín, BLAST, BeadStudio, BioEdit, Bootstrap, BrainVoyager, CLUMP, CSPRO, CellQuest, ClustalW, Cogent, Complex Samples, Complex samples, CubeX, DARTEL, DIVA-GIS, DTIFit, DTV.II SR, Datacam, Digilab, Digipro, E-Prime, EEGLab, EPI info, EXCEL, Epi Info, Epi-Info, EpiData, EpiInfo, EpiTools, Excel, EyeLink Data Viewer, EyeVision, FLIRT, FMRIB Software Library, FNIRT, FSL, FSL-VBM, FastQC, Firefox, GENECOUNTING, GENEPOP, GRIMP, GlobalWorks, Globalpark, GoldWave, Gower, GraphPad, HGF, HVS Image, Haploview, I-TASSER, ICC toolbox, IPA, Illustrator, Image J, Image lab, ImageJ, Imagelab, JMP, JWatcher, LI-toolbox, LISREL, LatentGold, Luminex 100 ™ IS, MASCOT, MATLAB, MCODE, MEGA, MELODIC, METAL, Mac, Mac OS, Mach, Mach2QTL, Macintosh, MapWin, Mapwin, Marsbar, MassARRAY Assay Design, MassARRAY Typer, Matlab, Med-PC, MedPC, MetaMorph, Mirdeep2, ModFit, Mplus, Muscle, NCSS, NIS, NLME, Network, NumPy, Nvivo, Office, PGA, PLINK, PPI Network, PRIMER, PROCESS, Patch Analyst, PhyML, Presentation, Primer, Primer-BLAST, Prism, Psychophysics Toolbox, Python, QGIS, Quantity One, Questionpro, R, R Studio, RevMan, SAS, SMART, SNAP, SPM, SPM anatomy toolbox, SPSS Amos, SQL, STAR, STATA, Samtools, SciPy, Scion image, Sequence Scanner, Sigma plot, SigmaStat, SignalP, Stata, Surfer, TANRIC, TAPAS, TBSS, Talairach Daemon, TargetScan, Trimmomatic, VBM, Vegan, Venny, Virtuoso, Visual C++, Volume 1, WFU pickatlas, WFU-Pickatlas, WinEEG, Windows, XLSTAT, Xena, dual regression, edge, edgeR, epidata, excel, gplots, iDataFax, iMap, miRDB, microRNA, nlme, sLORETA, vegan, voicebox, waver, windows

AFNI, Biotrace, Brainsight, Eyelink Toolbox, FSL, HGF, ISC-toolbox, Ledalab, MATLAB, Matlab, OS-X, QUEST, SPM, SPSS, TAPAS, ViewPoint, Windows

ANNOVAR, BCFtools, BEAGLE, BLAST, BOLT-LMM, BWA-MEM, BeadStudio, Birdseye, CNVmap, CoNIFER, ConQuest, DISSECT, GATK, GEMINI, GRIMP, GTX, GenCall, GeneOverlap, Genome Variation Server, Genome browser, HRC, IMPUTE, IPA, KING, MACH, MERLIN, METACARPA, METAL, MORGAN, Mach, Mach2QTL, Mutation Surveyor, PBAP, PEDSTATS, PLINK/SEQ, PennCNV, Picard, PolyPhen, Primer, Quanto, R, RUMM, SAMtools, SHAPEITv, SLINK, SMARTPCA, SNPTEST, SPSS Statistics, Seattle Seq, Variant Effect Predictor, XHMM, bedtools, cnvHap, cutadapt, eRM, ltm, mrsFAST, ordinal, rms, sickle

BLAST, FastQC, IPA, Image lab, MCODE, Mirdeep2, ModFit, PPI Network, Primer-BLAST, R, SPSS, STAR, Samtools, Trimmomatic, Venny, Xena, edge, edgeR, gplots, miRDB, microRNA, vegan

BeGaze, Enketo, Experiment Center, Open Data Kit, Prism, R, iView X

C, C++, OsiriX, REMIT, ReMIT, ReMIT Client, ReMITclient, dcm4che, dcm4chee

GitHub, MAGPIE

ArcGis, ENMtools, Google Earth, SDMtoolbox, Spatial Analyst

JAVA, Java, Java Runtime Environment, ProteoLens, Windows

MATLAB, NumPy, PsychoPy, Python, R, SPSS

MATLAB, Netcdf, PyMS, Pycdf, Pycluster, Python, R, SPSS, SciPy, matplotlib, tcl, tk

Access, Actiware, BioConductor, CCS, COLONY, Cervus, Cluster, EASY RA1 Easy Randomizer, Epi Info, Epidata, Excel, GIS, GSEA, Image-Pro Plus, J-Express, JMP, LAS, MAXQDA, MLwiN, OpenEpi, PABAK-OS calculator, PRIMER, PowerPoint, Questionpro, R, R Studio, RevMan, SPSS, STATA, SUDAAN, Stata, TreeView, Vegan, Win, Windows, dlnm

GitHub, Java, MySQL, Python, QuIN, THREaD Mapper Studio, Tomcat, iDREM, interactive DREM

GitHub, Linux, M-Track, MacOS X, OpenCV, Pathomx, PyPi, Python, Ubuntu, Windows

OntoFox

ANDES, ANNOVAR, ASCAT, Access, Analyst, Aninhado, ArcGIS, ArcMap, BCFtools, BLAST, BLASTp, BOLT-LMM, BWA, BWA-MEM, BioConductor, BioEdit, Bioanalyzer, Bioconductor, Bioplex Manager, Blast, Blastp, BrainStorm, C#, C++, C2, CALIB, CASAVA, CIBERSORT, CNVmap, CRAN, Calib, ChAMP, Chrome, ClustalW, Cluster, CoXpress, ConQuest, DESeq, DESeq2, DISSECT, Django, DriverNet, EdgeR, Enketo, Epi, EpiInfo, EpiR, EpiTools, EstimateS, Excel, Experiment Builder, FAP, FIMO, FastQC, FigureJ, Firefox, FlowJo, FunciSNP, G*Power, GATK, GDAL, GOseq, GRAB, GSEA, GTX, GenCall, Gene Cluster, GeneMapper, GeneOverlap, Genepix Pro, GenomeStudio, GitHub, H2O R interface, HRC, HTML, HTSeq, Haploview, IMPUTE, IPA, Image-Pro Plus, ImageJ, Immunoratio, Internet Explorer, J-Express, JAGS, JMP, Java, KING, KOBAS, Ki67 Vv, LAN toolbox, LAS, Linux, MACS, MATLAB, MCMCglmm, MEGA, METACARPA, METAL, MSIsensor, MSstats, Macintosh, MapInfo Professional, Matlab, Mice, Mirdeep2, Mixer, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NET, NLME, NetMHCpan, NumPy, Open Data Kit, Open Meta-Analyst, OpenCL, OptimalCutpoints, PABAK-OS calculator, PASW Statistics, PIVOT, PLINK, PLINK/SEQ, PRIMER, Pajek, Perl, PhosphOrtholog, Photofiltre, Photoshop, Picard, Pixelmator, Plink, PolyPhen, Polyphen, Polysolver, Primer, Primer-BLAST, Prism, ProctorU, Promasys, Python, QGIS, Quanto, R Studio, READ, REDCap, ROCR, RSeQC, RTA, RTN, RUMM, Rcpp, Remote Proctor Now, Revman, Rhtslib, Rstan, Rtsne, SAMtools, SAS, SHAPEITv, SMARTPCA, SNPTEST, SOCPROG, SPSS, SPSS Statistics, STAR, STATA, Safari, Sailfish, Salmon, Samtools, Scan, SciPy, Skyline, SnpEff, SomaticSignatures, Soscisurvey, Stan, Stata, Statistica, Subread, Survival, T-LoCoH, T3_MM, TargetScan, TopHat, ToppFun, TreeView, Treeview, Trim Galore!, Trimmomatic, VarScan, Vegan, VirtualBox, Visiopharm, Visual Basic, Visual Studio, Windows, XHMM, aLFQ, adjustedRandIndex, bam-readcount, bcl2fastq2, bedtools, bipartite, bnlearn, boot, car, clam, coXpress, consensus MIBC, cutadapt, dcGOR, dismo, dplyr, eRM, edge, edgeR, fmsb, gdata, ggplot2, ggsashimi, glmnet, gplots, gpu-lasso, gtools, h2oEnsemble, hgu95av2, hu6800, illuminaio, immunoSEQ Analyzer, jQuery, lattice, linux, lme4, lmer, ltm, map2stan, mgcv, miRDB, mice, mitml, netcarto, nlme, openMEEG, ordinal, pROC, plotrix, psych, quantregForest, raster, rgdal, rioja, rjags, rms, rpart, samtools, scPipe, sensitivity, sickle, skewer, sourceR, survC1, survival, survminer, tidyr, tximport, vcftools, vegan, windows, xCell

FlowJo, Statview, ToupView

GitHub, R, aLFQ, dcGOR

GPS Sample, STATA

GSEA, PyRadiomics, caret, irr, mRMRe, survcomp

CAD, CFD, Excel, Fiji, Imaris, LAS X, Med-PC, MedPC, Office, Photoshop, Prism, Quicktime, SPSS Statistics

C++, Linux, NFTsim, OpenSUSE

Stella

BD FACSDiva, BWA, BisoGenet, Cufflinks, Cytoscape, DAVID, DESeq, FIMO, FastQC, GOseq, GSEA-P, HTSeq, KOBAS, MACS, Perl, R, iGenomes, skewer

Autodock Vina, CellQuest, CompuSin, CompuSyn, InsightII, Prism, PyMOL, Quantity One, Vina

Chrome, Django, Firefox, HTML, Internet Explorer, PhosphOrtholog, Python, R, Safari, VirtualBox

Flash, MacVide, Matlab

3dBandpass, 3dDespike, AFNI, ANFI, BootES, DTIFit, Debian, FLIRT, FSL, MSM-All, MapIcosahedron, NeuroDebian, NeuroQuant, NeuroSynth, PyMVPA, Quarc, SAMSCo, SUMA

C, Java, Matlab, MetaSel, MicroSyn, NET, Python, R, Visual Basic, Visual Studio, Windows

C, C#, Photoshop, Pixelmator, R, WPS, WholePathwayScope, Window, Windows, lme4

DOGS, Java

3dBandpass, 3dDespike, AFNI, BootES, Debian, FSLView, FreeSurfer, MSM-All, MapIcosahedron, Mricron, NeuroDebian, Nilearn, PyMVPA, Python, SPM, SUMA, Scikit-learn

BEDTools, BLASR, Bioconductor, C, CapR, Chaste, GenomePop, Linux, MEDYAN, Mac, Mac OS X, MinGW-w64, NFTsim, OSX, Objective-C, OpenCL, OpenSUSE, OsiriX, PEPIS, Perl, PhysiCell, R, REMIT, RHEL, Rcpp, ReMIT, ReMIT Client, ReMITclient, Rhtslib, SSPACE-LongRead, Strawberry, VASP-E, VirtualBox, Windows, dcm4che, dcm4chee, g++, gcc, glmnet, gpu-lasso, linux, pSSAlib, scPipe

Macintosh, NLME, R, SAS, SPSS, SPSS Statistics, STATA, dlnm

LAILAPS-QSM

MEGA, SILVA SINA, Venny

3C Primer Design, 3PD, ASPASIA, AlignerBoost, C#, CBFA, DOGS, FigureJ, GLPK, GitHub, ImageJ, Immunoratio, JDK, Java Advanced Imaging, Java JRE, Java Runtime Environment, Java Virtual Machine, JavaScript, Javascript, Ki67 Vv, LAMINA, MAGERI, Mac OS, Matlab, MatrixConverter, MySQL, NET, NemaFootPrinter, OptFlux, Optflux, PathVisio, PathVisioRPC, Perl, Podbat, ProteoLens, Python, QuIN, R, RNA-SeQC, ROCR, SQL, Tomcat, UNIX, Visual Studio, Windows, iDREM, interactive DREM

ARLEQUIN, BEAST, BIOEDIT, Bioportal, CLUMPP, DISTRUCT, DIYABC, Datamonkey, FREENA, FSTAT, GENELAND, GENEMAPPER, GENEPOP, LAGRANGE, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, NETWORK, PAUP, PHASE, PhyML, SPAGeDI, STRUCTURE, TRACER, VIP

Digipro, SPSS

Access, Excel, MAXQDA, R, SAS, SPSS, SPSS Statistics, STATA, Stata, Windows, windows

BLAST, ClustalW, Datamonkey, Ensembl, GREAT, Geneious, HyPhy, MAGMA, MEGA, MrBayes

AMBERTOOLS, CPPTRAJ, Chimera, ORTEP, PASS, SADABS, SAINT, SHELXTL

Analyst, ArcView, Arlequin, Artemis, Bellerpheron, BioMart, BioTools, Biomart, Bioplex Manager, Bottleneck, Clustal, Clustal W, ClustalW, DNAsp, Datamonkey, DnaSP, EXCEL, Ensembl, Epi, EstimateS, FGENESB, FastQC, Fig Tree, Flex Analysis, Fstat, GenePop, Geneious, Geneland, Genome browser, GenomeStudio, GlobalWorks, Google Earth, HyPhy, I-TASSER, IBDWS, IPA, Image J, InterPro, LogCombiner, MASCOT, MEGA, MSstats, MUSCLE, Mirdeep2, Modeltest, MrBayes, Muscle, Mutation Surveyor, Network, OptimalCutpoints, PAUP*, PCORD, PLINK, Patch Analyst, Perl, PhyML, PhylopythiaS, PolyPhen, Primer, Primer-BLAST, Primer3 Input, ProteomeWeaver, PyroTagger, Q-LAB, R, RDP Classifier, SMART, SPSS, STAR, Samtools, SigmaPlot, SigmaStat, SignalP, Skyline, Structure, TargetScan, Tracer, TreeAnnotator, Trimmomatic, Vegan, beast, convert, edge, edgeR, genemapper, gplots, miRDB, migrate, vegan

3dFDR, AFNI, ArcGIS, Attivio, Bamgineer, BioPython, Biopython, C#, CLC Genomic Workbench, CNVkit, COBRAme, COBRApy, CellProfiler, Chrome, Django, ENCORE, Ensembler, EyeLink Data Viewer, FSLView, Fiji, Firefox, GARLI, GNU R, GRAB, GitHub, HDDM, HMMER, HTML, IDEPI, Internet Explorer, Inxight, Java, JavaScript, Linux, M-Track, MATLAB, MDAnalysis, Mac OS X, MacOS, MacOS X, Matlab, Matplotlib, MorphoLibJ, Mricron, NET, NLTK, Netcdf, NeuroSynth, Newbler, Nilearn, Novoalign, NumPy, OpenCV, Pathomx, Pep2Path, PhosphOrtholog, ProDy, PsychoPy, PyMS, PyPhi, PyPi, Pycdf, Pycluster, Qt, R, READ, Reportlab, SAMtools, SMRT analysis, SPM, SPSS, Safari, SciPy, Scikit-learn, THREaD Mapper Studio, Telescope, Ubuntu, VirtualBox, Visual Studio, Windows, Yahoo-BOSS, Yahoo-BOSS API, github, iMap, jQuery, joblib, matplotlib, samtools, scikit-learn, tcl, tk, vcftools

ANNOVAR, ASCAT, BCFtools, BEAGLE, BWA-MEM, CADD, CNVmap, ChAMP, CoNIFER, Condel, GEMINI, GeneOverlap, Geneious, Genome Analysis Toolkit, Genome Variation Server, GenomeStudio, ImageJ, MERLIN, MORGAN, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Novoalign, PBAP, PEDSTATS, PLINK, PLINK/SEQ, PennCNV, Picard, PolyPhen, Polyphen, Polysolver, Prism, R, REDCap, RTN, SAMtools, SLINK, Salmon, Seattle Seq, Sift, SnpEff, SomaticSignatures, Trim Galore!, VAX, VarScan, Variant Effect Predictor, Visiopharm, XHMM, bam-readcount, bcl2fastq2, bedtools, cnvHap, consensus MIBC, cutadapt, edgeR, mrsFAST, samtools, sickle, survival, survminer, tximport, xCell

ArcGIS, Biopython, CNVkit, Netcdf, NumPy, PyMS, Pycdf, Pycluster, Python, Reportlab, tcl, tk

GARLI, Newbler, Novoalign, Python, SAMtools, SMRT analysis, github

Statistica, qBase

Artemis, BLASTp, BioTools, FGENESB, Flex Analysis, MASCOT, PhylopythiaS, ProteomeWeaver, SigmaPlot, SigmaStat

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

BioEdit, EpiR, MEGA, ProctorU, QGIS, R, Remote Proctor Now, ggsashimi, mgcv

SPSS, Windows

Endnote

Arlequin, Arlequín, BioEdit, Network, SPSS, Sequence Scanner

Chrome, Django, Firefox, HTML, Internet Explorer, PhosphOrtholog, Python, R, VirtualBox, jQuery

Access, SPSS

BEAST, CLC Genomic Workbench, CRAN, Ensembler, GARLI, Java, JavaScript, Javascript, LabVIEW, M-Track, MAGPIE, MATLAB, Matlab, MultiTypeTree, MySQL, Newbler, Novoalign, OpenCV, PyPhi, Python, Qt, QuIN, R, Ruby on Rails, SAMtools, SMRT analysis, Tomcat, VDJtools, Wham, dcGOR, iDREM, interactive DREM

BD FACSDiva, BiNGO, Bioworks, BisoGenet, ClueGO, Cufflinks, DAVID, FastQC, FunRich, GSEA-P, MASCOT, Office Excel, Prism, Reactome, Tophat, clusterMaker, iGenomes

AFNI, ANFI, ART, Brain Vision Analyzer, CONN, CubeX, DTIFit, FDT, FLIRT, FNIRT, FSL-VBM, Fortran, FreeSurfer, ISC-toolbox, MATLAB, MELODIC, Psychophysics Toolbox, SAMSCo, SPM, SPSS, Stata, TBSS, TrackVis, VBM, ViewPoint, conn, dual regression

IVICT, MATLAB, Mechanical Turk, STRAIGHT, TurkPrime, articulatory synthesizer

Linux, MacOS X, Pathomx, PyPi, Python, Qt, Windows

ACME, ANDES, BLASR, C, C++, Chaste, CoXpress, DelPhi, Fortran, GenomePop, Image Processing Toolbox, MIiSR, Mac, Mac OS X, MacOS, MacOS X, MacOSX, Macintosh, Matlab, Mindboggle, NFTsim, NovoSNP, OpenSUSE, Pathomx, Pep2Path, Perl, PolyPhred, PyPi, Python, Qt, QuickPALM, R, RHEL, SNPdetector, SSPACE-LongRead, Telescope, Ubuntu, Unix, VASP-E, VirtualBox, Windows, biographer, cellXpress, coXpress, gcc, gdata, gplots, gtools, hgu95av2, hu6800, plotrix, windows

Artemis, BLASTp, BioTools, FGENESB, Flex Analysis, IPP, Image-Pro Plus, InterPro, MASCOT, Office Excel, Photoshop, PhylopythiaS, ProteomeWeaver, SPSS, Satistix, Scope-Pro, SigmaStat, Windows

CNVkit, HMMER, IDEPI, Python, Reportlab, VirtualBox, joblib, matplotlib, scikit-learn

AFNI, ART, AlphaSim, Anatomy atlas, CONN, Cyberball, DARTEL, E-Prime, E-prime, FSL, FSLView, Fieldmap, GoldWave, HGF, ICC toolbox, ISC-toolbox, LI-toolbox, MATLAB, Macintosh, MarsBar, Marsbar, MatLab, Matlab, Mricron, NeuroSynth, Nilearn, OS-X, Pickatlas, Presentation, Psychophysics Toolbox, Python, REST, SPM anatomy toolbox, SPSS, SPSS Statistics, Scikit-learn, TAPAS, Talairach Daemon, ViewPoint, WFU pickatlas, WFU-Pickatlas, WFU-pick atlas, Windows, conn, neurofeedback toolbox

BVQX, MATLAB, PASW Statistics, Presentation, SPSS Statistics, Tailarach Daemon

Arlequin, BLAST, Bottleneck, Clustal W, DnaSP, ENMtools, EXCEL, Fig Tree, Fstat, GenePop, Geneland, IBDWS, LogCombiner, MEGA, MaxEnt, Modeltest, MrBayes, Network, PAUP*, SDMtoolbox, Structure, Tracer, TreeAnnotator, beast, convert, genemapper, migrate

ANDES, BLASR, BWA, Bellerpheron, Blastn, C, C++, DESeq, DNAsp, EstimateS, FIMO, GOseq, Geneious, HTSeq, Java, KOBAS, Linux, MACS, MEGA, MUSCLE, NemaFootPrinter, NovoSNP, PCORD, PolyPhred, PoreWalker, PyroTagger, R, RDP Classifier, SNPdetector, SQL, SSPACE-LongRead, TopHat, UNIX, Unix, blastn, skewer

MATLAB

3dBandpass, 3dClustsim, 3dDeconvolve, 3dDespike, 3dDetrend, 3dFDR, 3dFWHMx, 3dmaskave, 3dttest+ +, BootES, Cogent, DTIFit, Debian, EyeLink Data Viewer, FLIRT, FSL, FreeSurfer, ISC-toolbox, MATLAB, MSM-All, MapIcosahedron, Matlab, NeuroDebian, NeuroSynth, Psychophysics Toolbox, PyMVPA, Python, SAMSCo, SPM, SPSS, SUMA, ViewPoint, iMap, waver

ARLEQUIN, Arlequin, BEAST, BIOEDIT, BLAST, Bioportal, Bottleneck, CLUMPP, Clustal W, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FREENA, FSTAT, Fig Tree, Fstat, GENEMAPPER, GENEPOP, GenePop, Google Earth, IBDWS, LAGRANGE, LogCombiner, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, Modeltest, MrBayes, NETWORK, Network, PAUP, PAUP*, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, Structure, TRACER, Tracer, TreeAnnotator, VIP, beast, convert, genemapper, migrate

Java, NemaFootPrinter, Perl, SPSS, Stata, UNIX

ArcGIS, R

BEAST, BIOEDIT, BLAST, BioEdit, Bioportal, Bottleneck, CLUMPP, Clustal W, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FREENA, FSTAT, Fig Tree, Fstat, GENELAND, GENEMAPPER, GENEPOP, GenePop, Geneland, Google Earth, IBDWS, LAGRANGE, LogCombiner, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, Modeltest, MrBayes, NETWORK, Network, PAUP, PAUP*, PHASE, PhyML, SPAGeDI, SPLITSTREE, SPSS, STATISTICA, STRUCTURE, SeqScape, Sequence Scanner, Structure, Surfer, TRACER, Tracer, TreeAnnotator, VIP, beast, convert, genemapper, migrate, mtPhyl

Analyst, BLASTp, Bioplex Manager, Epi, MSstats, R

IPA, Plink, R, RUMM, eRM, ltm

Nvivo, SPSS, SPSS Statistics

Chart, STATA

GitHub, Java, JavaScript, MySQL, QuIN

ArcMap, ENVI, EstimateS, Fragstats, LiDAR Analyst, Matplotlib, Maxent, Photofiltre, Python, R, STATA, Spatial Analyst, Spatial Statistics, Stata, Windows, lme4

AMBERTOOLS, CPPTRAJ, Chimera, CrystalClear, MOE, ORTEP, PASS, PLATON, SADABS, SAINT, Windows

ENSEMBLE, pCLAMP

Netcdf, NumPy, PyMS, Pycdf, Pycluster, Python, matplotlib, tk

SAS, SPSS, STATA, Stata, ZSCORE06

AMIX, CAD, CFD, CellProfiler, Chenomx, Chenomx NMR Suite, Cytobank, Illustrator, ImageJ, Imaris, LAS X, MATLAB, MorphoLibJ, Photoshop, Prism, Python, Quantity One, Quicktime, Rotor-Gene Q, SIMCA-P, TopSpin

ARLEQUIN, Arlequin, BEAST, BIOEDIT, BLAST, Bioportal, Bottleneck, CLUMPP, Clustal W, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FREENA, Fig Tree, GENELAND, GENEMAPPER, GENEPOP, GenePop, Geneland, Google Earth, IBDWS, LAGRANGE, LogCombiner, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, Modeltest, MrBayes, NETWORK, Network, PAUP, PAUP*, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, Structure, TRACER, Tracer, TreeAnnotator, VIP, beast, convert, genemapper, migrate

Acrobat, Bioanalyzer, CASAVA, CIBERSORT, Cluster, DESeq2, EdgeR, Gene Cluster, Genepix Pro, PIVOT, Prism, R, RSeQC, RTA, Rtsne, STAR, Sailfish, Statview, Subread, ToppFun, ToupView, TreeView, Treeview, immunoSEQ Analyzer

BLAST, Bellerpheron, BioMart, Biomart, Blastn, CADD, ClustalW, Condel, DNAsp, Datamonkey, EstimateS, GATK, Genome Analysis Toolkit, HyPhy, ImageJ, MEGA, MUSCLE, MrBayes, Novoalign, PCORD, Perl, Polyphen, Prism, PyroTagger, RDP Classifier, Sift, VAX, blastn

BLAST, Mutation Surveyor, PLINK, PolyPhen, Primer

SAS

STATA

Image J, Prism

Enketo, G*Power, R

2LD, Access, CLUMP, GENECOUNTING, GENEPOP, MassARRAY Assay Design, MassARRAY Typer, PGA, R, windows

E-Prime, Marsbar, Matlab, SPM, SPSS, Statistical Toolbox

R, mgcv, raster, rgdal

C++, OSX, PhysiCell, Windows, g++

Netcdf, NumPy, PyMS, Pycdf, Pycluster, Python, matplotlib, tcl

BLAST, DIVA-GIS, Excel, MEGA, Patch Analyst, QGIS, SPSS, SPSS Statistics

R, rjags

R, Revman

LAN toolbox, MATLAB, R, Scan, openMEEG

Excel

BD FACSDiva, BLAST, BisoGenet, Cufflinks, Cytoscape, DAVID, GSEA-P, IPA, Mirdeep2, Primer-BLAST, R, SPSS, STAR, Samtools, TargetScan, Tophat, Trimmomatic, edge, edgeR, gplots, iGenomes, miRDB, vegan

ARLEQUIN, ArcView, Arlequin, BEAST, BIOEDIT, BLAST, Bellerpheron, BioEdit, BioMart, Biomart, Bioportal, Blastn, Blastp, Bottleneck, CLUMPP, Clustal W, ClustalW, DISTRUCT, DIYABC, DNAsp, Datamonkey, DnaSP, EXCEL, EpiR, EstimateS, FREENA, FSTAT, Fig Tree, Fstat, GENELAND, GENEMAPPER, GENEPOP, GenePop, Geneious, Geneland, Google Earth, HyPhy, IBDWS, LAGRANGE, LogCombiner, MICRO-CHECKER, MODELTEST, MRBAYES, MUSCLE, Modeltest, Mothur, MrBayes, NETWORK, Network, PAUP, PAUP*, PCORD, PHASE, Patch Analyst, Perl, PhyML, Prism, PyroTagger, QGIS, R, RDP Classifier, SILVA SINA, SPAGeDI, SPLITSTREE, SPSS, STRUCTURE, Structure, TRACER, Tracer, TreeAnnotator, VIP, Vegan, Venny, beast, blastn, convert, genemapper, ggplot2, mgcv, migrate

CCS, SAS, STATA, Stata, runmlwin

BLAST, Bellerpheron, Blastn, ClustalW, DNAsp, EstimateS, Geneious, GlobalWorks, I-TASSER, MASCOT, MEGA, PCORD, Perl, PhyML, Prism, PyroTagger, RDP Classifier, SMART, SPSS, SignalP, blastn

NumPy, PyMS, Pycdf, Pycluster, Python, matplotlib, tcl, tk

C++, R, glmnet, gpu-lasso

CALIB, Strand7

CSPRO, Excel, MSOffice, SPSS, SPSS Statistics, Word

Altmetric, Chrome, Django, HTML, Internet Explorer, PhosphOrtholog, Python, R, SPSS, Safari, VirtualBox, jQuery

CLC Genomic Workbench, GARLI, Novoalign, Python, SAMtools, SMRT analysis, github

SAS

Chromeleon, LSM imaging

ARLEQUIN, Arlequin, BEAST, BIOEDIT, BLAST, Bioportal, Bottleneck, CLUMPP, Clustal W, DISTRUCT, DIYABC, Datamonkey, DnaSP, EXCEL, FREENA, FSTAT, Fig Tree, Fstat, GENELAND, GENEMAPPER, GENEPOP, GenePop, Geneland, Google Earth, IBDWS, LAGRANGE, LogCombiner, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, Modeltest, MrBayes, NETWORK, Network, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, Structure, TRACER, Tracer, TreeAnnotator, VIP, beast, convert, genemapper, migrate

Python, SciPy

Ensembl, Image J, Primer3 Input

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport, xCell

Excel

Biopython, CNVkit, Python, matplotlib

PRAAT, TurkPrime

Photoshop, R, Visual Basic, lme4

ANNOVAR, ASCAT, BCFtools, BLAST, BWA-MEM, CLC Genomic Workbench, CNVmap, ChAMP, FastQC, GARLI, GATK, GNU R, GRAB, GeneOverlap, GenomeStudio, IPA, MSIsensor, Mirdeep2, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Newbler, Novoalign, PLINK, PLINK/SEQ, Picard, PolyPhen, Polyphen, Polysolver, Primer-BLAST, Python, R, READ, REDCap, RTN, SMRT analysis, SPSS, STAR, Salmon, SnpEff, SomaticSignatures, TargetScan, Trim Galore!, Trimmomatic, VarScan, Visiopharm, XHMM, bam-readcount, bcl2fastq2, bedtools, consensus MIBC, cutadapt, edge, edgeR, github, gplots, miRDB, sickle, survival, survminer, tximport, vcftools, vegan, xCell

CALIB, Mimics

SAS

CBFA, GLPK, Java, Java JRE, Mac OS, OptFlux, Optflux

GitHub, MATLAB, Matlab

Artemis, BLASTp, BioTools, FGENESB, Flex Analysis, IPP, Image-Pro Plus, InterPro, MASCOT, Office Excel, Photoshop, PhylopythiaS, ProteomeWeaver, SPSS, Satistix, Scope-Pro, SigmaPlot, Windows

Acrobat, FlowJo, ToupView

Excel

3dBandpass, 3dDespike, AFNI, BootES, FreeSurfer, MSM-All, MapIcosahedron, NeuroDebian, NeuroSynth, PyMVPA, SUMA

Django, Firefox, HTML, Internet Explorer, PhosphOrtholog, Python, R, Safari, VirtualBox, jQuery

DTV.II SR, MetaMorph, Primer, SPSS, Volume 1

R2WinBUGS

Attivio, Inxight, NLTK, Python

ATLAS.ti, EpiInfo, Excel, Haploview, R, SAS, SPSS, SPSS Statistics, Windows

C, DelPhi, FLIRT, FSL, Linux, Mac, Windows

CBFA, JDK, Java, Java JRE, Mac OS, OptFlux, Optflux

Chrome, Firefox, HTML, Internet Explorer, PhosphOrtholog, Python, R, Safari, VirtualBox, jQuery

Matlab, SPSS Statistics

GitHub, Java, JavaScript, QuIN, Tomcat

BCFtools, BWA-MEM, CNVmap, GATK, GeneOverlap, PLINK, PLINK/SEQ, Picard, R, SAMtools, XHMM, bedtools, cutadapt, sickle

Arlequin, BLAST, BioMart, Biomart, Blastp, Bottleneck, Datamonkey, DnaSP, EXCEL, Fig Tree, Fstat, GenePop, Geneious, Geneland, GlobalWorks, Google Earth, HyPhy, I-TASSER, IBDWS, LogCombiner, MASCOT, MEGA, Modeltest, MrBayes, Muscle, Network, PAUP*, PhyML, R, SMART, SPSS, SignalP, Structure, Tracer, TreeAnnotator, Vegan, beast, convert, genemapper, migrate

Chrome, Django, Firefox, Internet Explorer, PhosphOrtholog, Python, R, Safari, VirtualBox, jQuery

Aninhado, R, bipartite, netcarto

Bellerpheron, Blastn, DNAsp, EstimateS, Geneious, MEGA, MUSCLE, Perl, PyroTagger, RDP Classifier, blastn

Excel

Java

Prism

BOTTLENECK, COLONY, GENEPOP, GenAlEx, Genescan, MICROCHECKER, MLRELATE, Peakscanner

BOTTLENECK, COANCESTRY, Cervus, GENEPOP, GenAlEx, Genescan, MICROCHECKER, MLRELATE, Peakscanner, SAS

ARLEQUIN, BEAST, BIOEDIT, Bioportal, CLUMPP, DISTRUCT, DIYABC, Datamonkey, FSTAT, GENELAND, GENEMAPPER, GENEPOP, LAGRANGE, MEGA, MICRO-CHECKER, MODELTEST, MRBAYES, NETWORK, PAUP, PHASE, PhyML, SPAGeDI, SPLITSTREE, STRUCTURE, TRACER, VIP

ASCAT, ChAMP, GATK, GenomeStudio, MSIsensor, MuPeXI, MuTect, MutationAssessor, MutationalPatterns, NetMHCpan, Picard, PolyPhen, Polyphen, Polysolver, R, REDCap, RTN, Salmon, SnpEff, SomaticSignatures, Trim Galore!, VarScan, Visiopharm, bam-readcount, bcl2fastq2, consensus MIBC, edgeR, samtools, survival, survminer, tximport

Image lab, MCODE, ModFit, PPI Network, SPSS, TargetScan, Venny, miRDB, microRNA