| TCR repertoire |
MiTCR36
|
http://mitcr.milaboratory.com/ |
|
Decombinator101
|
https://github.com/uclinfectionimmunity/Decombinator |
|
iSSAKE102
|
ftp://ftp.bcgsc.ca/supplementary/iSSAKE/ |
|
IMGT or HIGHV-Quest37
|
http://www.imgt.org/HighV-QUEST/ |
| Antibody repertoire |
IMGT or HIGHV-Quest37
|
http://www.imgt.org/HighV-QUEST/ |
|
IgTree103
|
http://immsilico2.lnx.biu.ac.il/Software.html |
|
VDJFasta104
|
http://sourceforge.net/projects/vdjfasta/ |
| RNA-seq105
|
VarScan106
|
http://varscan.sourceforge.net/ |
|
GATK107
|
http://www.broadinstitute.org/gatk/ |
|
SAMtools108
|
http://samtools.sourceforge.net/ |
|
ERANGE40
|
http://woldlab.caltech.edu/rnaseq |
|
Scripture109
|
http://www.broadinstitute.org/software/scripture/ |
|
Cufflinks45
|
http://cufflinks.cbcb.umd.edu/ |
|
CuffDiff45
|
http://cufflinks.cbcb.umd.edu/ |
|
EdgeR46
|
http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html |
|
DESeq49
|
http://www.bioconductor.org/packages/release/bioc/html/DESeq.html |
|
Myrna110
|
http://bowtie-bio.sourceforge.net/myrna/index.shtml |
|
PoissonSeq48
|
http://cran.r-project.org/web/packages/PoissonSeq/index.html |
| ChIP-seq105,111
|
ERANGE40
|
http://woldlab.caltech.edu/rnaseq |
|
CisGenome112
|
http://www.biostat.jhsph.edu/~hji/cisgenome/ |
|
MACS113
|
http://liulab.dfci.harvard.edu/MACS/ |
|
PeakSeq114
|
http://info.gersteinlab.org/PeakSeq/ |
|
SPP115
|
http://compbio.med.harvard.edu/Supplements/ChIP-seq/ |
| eQTL |
MatrixEQTL58
|
http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/ |
|
PLINK116
|
http://pngu.mgh.harvard.edu/~purcell/plink/ |
|
R/qtl117
|
http://www.rqtl.org/ |
|
snpMatrix118
|
http://www.bioconductor.org/packages/2.3/bioc/html/snpMatrix.html |
| Networks |
WGCNA82
|
http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/ |
|
coXpress119
|
http://coxpress.sourceforge.net/ |
|
Inferelator120
|
http://bonneaulab.bio.nyu.edu/networks.html |
|
ARACNE121
|
http://wiki.c2b2.columbia.edu/workbench/index.php/ARACNe/ |
|
RimbaNET87
|
http://icahn.mssm.edu/departments-and-institutes/genomics/about/software/rimbanet/ |
| Cytometry63
|
FlowMeans122
|
http://www.bioconductor.org/packages/release/bioc/html/flowMeans.html |
|
FLAME123
|
http://www.broadinstitute.org/cancer/software/genepattern/modules/FLAME/ |
|
FLOCK124
|
https://immport.niaid.nih.gov/immportWeb/analysis/flow/displayOverview.do?method=displayFlockOverview |
|
SamSPECTRAL125
|
http://www.bioconductor.org/packages/devel/bioc/html/SamSPECTRAL.html |
|
SPADE64
|
http://www.bioconductor.org/packages/release/bioc/html/spade.html |
|
|
http://cytospade.org/ |
|
viSNE66
|
http://www.c2b2.columbia.edu/danapeerlab/html/cyt.html |
| Visualization |
Cytoscape93
|
http://www.cytoscape.org/ |
|
Gephi |
https://gephi.org/ |
|
Circos126
|
http://circos.ca/ |
| Databases or online tools |
ImMunoGeneTics127
|
http://www.imgt.org/ |
|
ImmPort |
https://immport.niaid.nih.gov/ |
|
MsigDB53
|
http://www.broadinstitute.org/gsea/msigdb/index.jsp |
|
GenePattern54
|
http://www.broadinstitute.org/cancer/software/genepattern/ |
|
DAVID55,56
|
http://david.abcc.ncifcrf.gov/ |
|
Stanford Data Miner128
|
|
|
Structure129
|
http://pritchardlab.stanford.edu/structure.html |
|
PCAdmix |
https://sites.google.com/site/pcadmix/home |
|
myPEG130
|
http://www.megasoftware.net/myPEG/myPEG.php |
|
GWASdb131
|
http://jjwanglab.org/gwasdb/ |
|
HaploReg132
|
http://www.broadinstitute.org/mammals/haploreg/haploreg.php |
|
RegulomeDB133
|
http://regulomedb.org/ |
|
GRAIL134
|
http://www.broadinstitute.org/mpg/grail/ |
|
DGIdb135
|
http://dgidb.genome.wustl.edu/ |
|
GSEA50
|
http://www.broadinstitute.org/gsea/index.jsp |
|
ProfileChaser136
|
http://profilechaser.stanford.edu/ |
|
LINCS browser137,138
|
http://lincs.hms.harvard.edu/explore/pathway/ |
|
|
http://lincs.hms.harvard.edu/explore_/canvasbrowser/ |
