standarized name	project url	reference / doi
3D Slicer	https://www.slicer.org	https://doi.org/10.1016/j.mri.2012.05.001
3USS	http://www.biocomputing.it/3uss_server	10.1093/bioinformatics/btv035
ADAPTS	https://github.com/sdanzige/ADAPTS	10.1371/journal.pone.0224693
affy	https://www.bioconductor.org/packages/release/bioc/html/affy.html	https://doi.org/doi:10.18129/B9.bioc.affy
AltAnalyze	https://github.com/nsalomonis/altanalyze	https://doi.org/10.1093/nar/gkq405
ANNOVAR	https://github.com/GuoPan1992/ANNOVAR	https://doi.org/10.1093/nar/gkq603
APAtrap		10.1093/bioinformatics/bty029 
Apriori		http://www.columbia.edu/~rd2537/docu/apriori(abstract).pdf
ASAP	http://github.com/DeplanckeLab/ASAP	10.1093/bioinformatics/btx337 
BackSPIN	https://github.com/linnarsson-lab/BackSPIN	10.1126/science.aaa1934 
BayesSpace	https://www.bioconductor.org/packages/release/bioc/html/BayesSpace.html	https://doi.org/10.1038/s41587-021-00935-2
BBrowser	https://data.humancellatlas.org/analyze/portals/bioturing-browser	
BCconf	https://github.com/chrismckennan/BCconf	" 	
https://doi.org/10.48550/arXiv.1801.00865"
bcl2fastq	https://github.com/brwnj/bcl2fastq	
BEDTools	https://github.com/arq5x/bedtools2	
BioJupies	https://github.com/MaayanLab/biojupies	10.1016/j.cels.2018.10.007
BIONJ		10.1093/oxfordjournals.molbev.a025808 
bismark	https://github.com/projectbismark/bismark	https://doi.org/10.1093/bioinformatics/btr167
BLAST	https://blast.ncbi.nlm.nih.gov/Blast.cgi	https://doi.org/10.1093/nar/gkn201
Bowtie	https://github.com/BenLangmead/bowtie	10.1186/gb-2009-10-3-r25 
BRIE	http://github.com/huangyh09/brie	https://doi.org/10.1186/s13059-017-1248-5
bseqsc	https://github.com/shenorrLabTRDF/bseqsc	
bumphunter	https://github.com/rafalab/bumphunter	https://doi.org/doi:10.18129/B9.bioc.bumphunter
bustools	https://github.com/FlyingCampDesign/bustools.git	
BVS-CLR		10.1515/ijb-2016-0043
BWA	http://bio-bwa.sourceforge.net/	10.1093/bioinformatics/btp324
CallMarker	http://biocc.hrbmu.edu.cn/CellMarker/	https://doi.org/10.1093/nar/gky900
cate		10.1214/16-AOS1511
Cell Ranger	https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger	
cell2location	https://github.com/BayraktarLab/cell2location	https://doi.org/10.1038/s41587-021-01139-4
CellPhoneDB	https://github.com/Teichlab/CellPhoneDB	10.1038/s41596-020-0292-x
celltalker	https://github.com/arc85/celltalker	
cellxgene	https://github.com/chanzuckerberg/cellxgene	
ChAMP	https://www.bioconductor.org/packages/release/bioc/html/ChAMP.html	https://doi.org/doi:10.18129/B9.bioc.ChAMP
changepoint		10.1093/bioinformatics/btu189
chromVAR	https://bioconductor.org/packages/release/bioc/html/chromVAR.html	doi:10.1038/nmeth.4401
CIBERSORT	https://github.com/zomithex/CIBERSORT	https://doi.org/10.1038/nmeth.3337
CIDR	https://github.com/VCCRI/CIDR	https://doi.org/10.1186/s13059-017-1188-0
CITE-seq-counter	https://sites.google.com/site/fredsoftwares/products/cite-seq-counter	https://doi.org/10.1093/nargab/lqaa025
CLARANS		https://dl.acm.org/doi/10.1109/TKDE.2002.1033770
ClustVis	https://github.com/taunometsalu/ClustVis	
ComBat		10.1093/biostatistics/kxj037
COMET	https://github.com/MSingerLab/COMETSC	10.15252/msb.20199005
ComICS	https://cran.r-project.org/web/packages/ComICS/index.html	
ConsensusClusterPlust	https://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html	
CorrConf	https://github.com/chrismckennan/CorrConf	https://doi.org/10.48550/arXiv.1808.05895
COTAN	http://bioconductor.org/packages/release/bioc/manuals/COTAN/man/COTAN.pdf	https://doi.org/10.1093/nargab/lqab072
csSAM	https://github.com/shenorrLabTRDF/csSAM	10.1038/nmeth.1439
Cufflinks	https://github.com/aveillady/Cufflinks	https://doi.org/10.1038/nprot.2012.016
Cutadapt	http://code.google.com/p/cutadapt/	https://doi.org/10.14806/ej.17.1.200
Cytobank	http://www.cytobank.org/index.html	
Cytoscape	https://cytoscape.org	https://doi.org/10.1101/gr.1239303
DaPars	https://github.com/ZhengXia/dapars	https://doi.org/10.1038/ncomms6274
DAVID	https://david.ncifcrf.gov	10.1038/nprot.2008.211
DDRTree	https://cran.r-project.org/web/packages/DDRTree/index.html	
DeconRNASeq	https://www.bioconductor.org/packages/release/bioc/html/DeconRNASeq.html	https://doi.org/10.1093/bioinformatics/btt090
desc	https://github.com/eleozzr/desc	https://doi.org/10.1038/s41467-020-15851-3
DESeq2	https://github.com/mikelove/DESeq2	https://doi.org/doi:10.18129/B9.bioc.DESeq2
Desingle	https://bioconductor.org/packages/release/bioc/html/DEsingle.html	https://doi.org/10.1093/bioinformatics/bty332
divo	https://cran.r-project.org/web/packages/divo/index.html	
DNAmtl		10.18632/aging.102173
DPT	http://www.helmholtz-muenchen.de/icb/dpt	https://doi.org/10.1038/nmeth.3971
dSVA	https://cran.r-project.org/web/packages/dSVA/dSVA.pdf	
DWLS	https://github.com/dtsoucas/DWLS	https://doi.org/10.1038/s41467-019-10802-z
edgeR	https://www.bioconductor.org/packages/release/bioc/html/edgeR.html	https://doi.org/doi:10.18129/B9.bioc.edgeR
enrichplot	https://www.bioconductor.org/packages/release/bioc/html/enrichplot.html	https://doi.org/doi:10.18129/B9.bioc.enrichplot
Enrichr	https://github.com/yokuyuki/Enrichr	https://doi.org/10.1186/1471-2105-14-128
ESTIMATE	https://bioinformatics.mdanderson.org/public-software/estimate/	https://doi.org/10.1038/ncomms3612
FastProject	https://github.com/YosefLab/FastProject	https://doi.org/10.1186/s12859-016-1176-5
FastQC	https://github.com/s-andrews/FastQC	
featureCounts	https://github.com/byee4/featureCounts	10.1093/bioinformatics/btt656
FIMO	https://meme-suite.org/meme/doc/fimo.html	10.1093/bioinformatics/btr064
FlowJo	https://www.flowjo.com/solutions/flowjo	
FVFC		10.1155/2017/3035481
g:Profiler	http://biit.cs.ut.ee/gprofiler/	
GATK	https://software.broadinstitute.org/gatk/	https://doi.org/10.1101/gr.107524.110
gEAR	https://github.com/IGS/gEAR	https://doi.org/10.1038%2Fs41592-021-01200-9
genefu	https://www.bioconductor.org/packages/release/bioc/html/genefu.html	https://doi.org/doi:10.18129/B9.bioc.genefu
GeneHancer		10.1093/database/bax028
GeneMANIA	http://genemania.org	10.1093/nar/gkq537
GenePattern	https://www.genepattern.org/#gsc.tab=0	10.1038/ng0506-500
GenomicAlignments	https://bioconductor.org/packages/release/bioc/html/GenomicAlignments.html	
GEOQuery		10.1093/bioinformatics/btm254
Gephi	https://gephi.org	
ggfortify	https://github.com/sinhrks/ggfortify	http://dx.doi.org/10.32614/RJ-2016-060
ggplot2	http://ggplot2.tidyverse.org	
ggpubr	https://cran.r-project.org/web/packages/ggpubr/index.html	
ggsashimi	https://github.com/guigolab/ggsashimi	https://doi.org/10.1371/journal.pcbi.1006360
Giotto	https://github.com/RubD/Giotto	https://doi.org/10.1186/s13059-021-02286-2
GISTIC		doi: 10.1186/gb-2011-12-4-r41
GOrilla	https://cbl-gorilla.cs.technion.ac.il/	https://doi.org/10.1186/1471-2105-10-48
Gpfates	https://github.com/Teichlab/GPfates	https://doi.org/10.1126/sciimmunol.aal2192
Granatum	http://garmiregroup.org/granatum/app	https://doi.org/10.1186/s13073-017-0492-3
GraphPad Prism	https://www.graphpad.com	
gsea	https://pypi.org/project/gsea	
GSVA	https://www.bioconductor.org/packages/release/bioc/html/GSVA.html	https://doi.org/doi:10.18129/B9.bioc.GSVA
Harmony	https://github.com/immunogenomics/harmony	https://doi.org/10.1038/s41592-019-0619-0
HISAT2	http://daehwankimlab.github.io/hisat2/	https://doi.org/10.1038/s41587-019-0201-4
Histocat		https://doi.org/10.1038/nmeth.4391
HOMER		10.1016/j.molcel.2010.05.004
HTSeq	https://github.com/brenninc/HTSeq	
iCellR	https://github.com/rezakj/iCellR	https://doi.org/10.1158/2159-8290.CD-21-0369
Integrative Genomics Viewer	https://github.com/igvteam/igv	
ImageJ		10.1186/s12859-017-1934-z
IntMAP		10.1093/nar/gky340
iSEE	http://bioconductor.org/packages/release/bioc/html/iSEE.html	https://doi.org/10.12688/f1000research.14966.1
ISnorm		https://doi.org/10.1093/nargab/lqaa059
ISOP	https://github.com/nghiavtr/ISOP	https://doi.org/10.1093/bioinformatics/bty100
JMP	http://www.jmp.com/en_us/software/jmp.html	
jvenn	https://jvenn.toulouse.inra.fr/app/index.html	https://doi.org/10.1186%2F1471-2105-15-293
Kallisto	https://pachterlab.github.io/kallisto/about	10.1038/nbt.3519
Kraken	http://www.ebi.ac.uk/research/enright/software/kraken	10.1016/j.ymeth.2013.06.027
liayson	https://cran.r-project.org/web/packages/liayson/index.html	https://doi.org/10.1101/445932
lifelines	https://pypi.org/project/lifelines	
Liger	https://github.com/cran/liger	https://doi.org/10.5281/zenodo.887386
limma	https://www.bioconductor.org/packages/release/bioc/html/limma.html	https://doi.org/doi:10.18129/B9.bioc.limma
lmQCM	https://cran.r-project.org/web/packages/lmQCM/index.html	https://doi.org/10.4137/CIN.S14021
loom-viewer	https://github.com/linnarsson-lab/loom-viewer	
Loupe Browser	https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/what-is-loupe-cell-browser	
lumi	https://www.bioconductor.org/packages/release/bioc/html/lumi.html	https://doi.org/doi:10.18129/B9.bioc.lumi
MACS	https://pypi.org/project/MACS	https://doi.org/10.1186/gb-2008-9-9-r137
maftools	https://www.bioconductor.org/packages/release/bioc/html/maftools.html	https://doi.org/doi:10.18129/B9.bioc.maftools
Mandalorion	https://github.com/rvolden/Mandalorion	
Mapper		10.2312/SPBG/SPBG07/091-100
MAST	https://www.bioconductor.org/packages/release/bioc/html/MAST.html	https://doi.org/doi:10.18129/B9.bioc.MAST
MatrixEQTL	https://cran.r-project.org/web/packages/MatrixEQTL/index.html	https://doi.org/10.1093/bioinformatics/bts163
Metascape	http://metascape.org/	https://doi.org/10.1038/s41467-019-09234-6
MFA	http://www.bioconductor.org/packages/devel/bioc/vignettes/mfa/inst/doc/introduction_to_mfa.html	
millefy	https://github.com/yuifu/millefy	https://doi.org/10.5281/zenodo.3591096
minfi	https://www.bioconductor.org/packages/release/bioc/html/minfi.html	https://doi.org/doi:10.18129/B9.bioc.minfi
MISO	https://github.com/yarden/MISO	https://doi.org/10.1038/nmeth.1528
MISTy		https://doi.org/10.1186/s13059-022-02663-5
mnnCorrect	https://rdrr.io/bioc/batchelor/man/mnnCorrect.html	https://doi.org/10.1038/nbt.4091
Monocle	http://cole-trapnell-lab.github.io/monocle-release/	https://doi.org/10.1038/nbt.2859
Morpheus	https://software.broadinstitute.org/morpheus/	
MouseNetV2	https://www.inetbio.org/mousenet/	
mpath		https://doi.org/10.1038/ncomms11988
MRMD	http://lab.malab.cn/soft/MRMD/contact.html	https://doi.org/10.1016/j.neucom.2014.12.123
mRMR	http://home.penglab.com/proj/mRMR/	https://doi.org/10.1142/s0219720005001004
MUSIC	https://github.com/Telethon-helper/MUSIC	
MuTect		10.1038/nbt.2514
p-hipster	http://phipster.org/	https://doi.org/10.1016/j.cell.2019.08.005
PAGODA	http://pklab.med.harvard.edu/scde/pagoda.links.html	10.1038/nmeth.3734
pamr	https://cran.r-project.org/web/packages/pamr/index.html	
PanglaoDB	https://panglaodb.se/	10.1093/database/baz046
pheatmap	https://cran.r-project.org/web/packages/pheatmap/index.html	
PhenoAgeAccel 		10.1371/journal.pmed.1002718
PhenoGraph	https://pypi.org/project/PhenoGraph	10.1016/j.cell.2015.05.047
phenoTest	https://www.bioconductor.org/packages/release/bioc/html/phenoTest.html	
Picard	https://broadinstitute.github.io/picard/	
PISA	https://github.com/shiquan/PISA	https://doi.org/10.1093/bioinformatics/btac562
PLAGE		https://doi.org/10.1186/1471-2105-6-225
Polyester	https://bioconductor.org/packages/release/bioc/manuals/polyester/man/polyester.pdf	https://doi.org/10.1093/bioinformatics/btv272
PQL		https://doi.org/10.1198/jcgs.2009.07118
prcomp	https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/prcomp	
profvis	https://cran.r-project.org/package=profvis	
pseudogp	https://github.com/kieranrcampbell/pseudogp	https://doi.org/10.1371%2Fjournal.pcbi.1005212
RaceID	https://cran.r-project.org/web/packages/RaceID/index.html	https://doi.org/10.1038/nature14966
RBPDB	http://rbpdb.ccbr.utoronto.ca/	https://doi.org/10.1093/nar/gkq1069
RCTD		10.1038/s41587-021-00830-w
RetNet	https://web.sph.uth.edu/RetNet/	
RNASeQC	https://github.com/francois-a/rnaseqc	
RPCLR	https://rdrr.io/cran/RPCLR/	
RSEM	https://github.com/deweylab/RSEM	https://doi.org/10.1186/1471-2105-12-323
Rsubread	https://www.bioconductor.org/packages/release/bioc/html/Rsubread.html	https://doi.org/doi:10.18129/B9.bioc.Rsubread
RUVSeq	https://bioconductor.org/packages/release/bioc/html/RUVSeq.html	https://doi.org/10.1038/nbt.2931
safe	https://www.bioconductor.org/packages/release/bioc/html/safe.html	https://doi.org/doi:10.18129/B9.bioc.safe
Sambamba	http://www.open-bio.org/wiki/Sambamba	https://doi.org/10.1093%2Fbioinformatics%2Fbtv098
SAMtools	http://samtools.sourceforge.net	10.1093/bioinformatics/btp352
SAVER		https://doi.org/10.1038/s41592-018-0033-z
SC3	https://www.bioconductor.org/packages/release/bioc/html/SC3.html	https://doi.org/doi:10.18129/B9.bioc.SC3
scanpy	https://github.com/theislab/scanpy	https://doi.org/10.1186/s13059-017-1382-0
scAPAmod		10.3390/ijms23158123
scDA		10.1016/j.csbj.2021.05.046
scDAPA		10.1093/bioinformatics/btz701
scDeppCluster	https://github.com/ttgump/scDeepCluster	https://doi.org/10.1038/s42256-019-0037-0
sceasy	https://github.com/cellgeni/sceasy	
SCENIC		https://doi.org/10.1038/nmeth.4463
scEntropy	https://github.com/jzlei/scEntropy	10.1142/s1793048020500010
scID		10.1016/j.isci.2020.100914
scImpute	https://github.com/Vivianstats/scImpute	https://doi.org/10.1038/s41467-018-03405-7
scLVM	https://github.com/PMBio/scLVM	10.1038/nbt.3102
scMapper	https://cran.r-project.org/web/packages/scMappR/index.html	https://doi.org/10.1093/nargab/lqab011
scMerge	https://www.bioconductor.org/packages/release/bioc/html/scMerge.html	https://doi.org/10.1073/pnas.1820006116
SCnorm	https://www.bioconductor.org/packages/release/bioc/html/SCnorm.html	https://doi.org/10.1038/nmeth.4263
scone	https://www.bioconductor.org/packages/release/bioc/html/scone.html	https://doi.org/doi:10.18129/B9.bioc.scone
Scope		https://doi.org/10.1038/s41596-021-00616-z
scran	https://www.bioconductor.org/packages/release/bioc/html/scran.html	https://doi.org/doi:10.18129/B9.bioc.scran
scSDAE		10.3390/genes11050532
scSVA	https://github.com/klarman-cell-observatory/scSVA	
sctransform	https://github.com/satijalab/sctransform	
scVAE	https://github.com/scvae/scvae	
scziDesk	https://github.com/xuebaliang/scziDesk	
Seurat	https://github.com/satijalab/seurat	
Sierra	https://github.com/VCCRI/Sierra	
Signac	https://github.com/timoast/signac	
SIMLR	https://bioconductor.org/packages/release/bioc/html/SIMLR.html	
Single Cell Signature Explorer		10.1093/nar/gkz601
Single Cell Virtual Cytometer	https://github.com/FredPont/single-cell-virtual-cytometer	
SingleR	https://bioconductor.org/packages/devel/bioc/vignettes/SingleR/inst/doc/SingleR.html	
SingleSplice	https://github.com/jw156605/SingleSplice	
Slingshot	https://github.com/SparkDevNetwork/Slingshot	
SMILE	https://github.com/rpmccordlab/SMILE	
SOUP		https://doi.org/10.1073/pnas.1817715116
SpaCell		https://doi.org/10.1093/bioinformatics/btz914
SPAdes		10.1089/cmb.2013.0084
SpaGCN		https://doi.org/10.1038/s41592-021-01255-8
SpaOTsc	https://github.com/zcang/SpaOTsc	
SPARK	https://github.com/xzhoulab/SPARK	
SparseDC	https://cran.r-project.org/web/packages/SparseDC/index.html	
SpatialDE		https://doi.org/10.1038/nmeth.4636
SpatialDWLS		10.1186/s13059-021-02362-7
Splatter		https://doi.org/10.1186/s13059-017-1305-0
Splotch		https://doi.org/10.1101/757096
SPOTlight	https://bioconductor.org/packages/devel/bioc/vignettes/SPOTlight/inst/doc/SPOTlight_kidney.html	https://doi.org/10.1093/nar/gkab043
SPRING	https://github.com/AllonKleinLab/SPRING	https://doi.org/10.1093/bioinformatics/btx792
squidpy	https://squidpy.readthedocs.io/en/stable/	
SSCA		https://doi.org/10.1142/9789813279827_0034
ssGSEA	https://github.com/broadinstitute/ssGSEA2.0	
STAR	https://github.com/alexdobin/STAR	https://doi.org/10.1093/bioinformatics/bts635
Star-Fusion	https://github.com/STAR-Fusion/STAR-Fusion	
StarSolo	https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md	http://dx.doi.org/10.1101/2021.05.05.442755
STARTRAC	https://github.com/Japrin/STARTRAC	https://doi.org/10.1038/s41586-018-0694-x
Stereoscope		https://doi.org/10.1038/s42003-020-01247-y
stLearn	https://stlearn.readthedocs.io/en/latest/	
STRING	https://string-db.org/	
STUtility	https://github.com/jbergenstrahle/STUtility	
Subread	https://github.com/machalen/Subread	
survival	https://github.com/therneau/survival	
survminer	https://cran.r-project.org/web/packages/survminer/index.html	
sva	https://www.bioconductor.org/packages/release/bioc/html/sva.html	https://doi.org/doi:10.18129/B9.bioc.sva
t-SNE		https://doi.org/10.48550/arXiv.2105.07536
Tangram	https://github.com/sonnyp/Tangram	
TargetScan	https://github.com/alex123012/TargetScan	
TECtool		https://doi.org/10.1038/s41592-018-0114-z
TMAP	https://github.com/iontorrent/TMAP	
Toppgene	https://toppgene.cchmc.org	https://doi.org/10.1093/nar/gkp427
Topslam		https://doi.org/10.1101/057778
Tracer	https://github.com/Teichlab/tracer	https://doi.org/10.1038/nmeth.3800
Trendsceek	https://github.com/edsgard/trendsceek	https://doi.org/10.1038/nmeth.4634
Trim Galore	https://github.com/FelixKrueger/TrimGalore	
Trimmomatic	https://github.com/usadellab/Trimmomatic	
TSCAN	https://github.com/zji90/TSCAN	https://doi.org/10.1093/nar/gkw430
UCSC genome browser	http://genome.ucsc.edu	10.1093/bib/bbs038
UMAP	https://github.com/lmcinnes/umap	https://doi.org/10.48550/arXiv.1802.03426
universalmotif	https://www.bioconductor.org/packages/release/bioc/html/universalmotif.html	https://doi.org/doi:10.18129/B9.bioc.universalmotif
UpSet	https://upset.app	
VALERIE	https://cran.r-project.org/web/packages/VALERIE/index.html	https://doi.org/10.1371/journal.pcbi.1008195
Velocyto	https://github.com/velocyto-team/velocyto.R	
viper	https://www.bioconductor.org/packages/release/bioc/html/viper.html	https://doi.org/doi:10.18129/B9.bioc.viper
Viral-Track	https://github.com/PierreBSC/Viral-Track	
Wanderlust	https://github.com/Riya-11/Wanderlust	
Waterfall		10.1016/j.stem.2015.07.013
WemIQ		10.1093/bioinformatics/btu757 
WGCNA	https://cran.r-project.org/web/packages/WGCNA/	
Wishbone	https://github.com/ManuSetty/wishbone	https://doi.org/10.1038%2Fnbt.3569
WL2Boost		https://doi.org/10.1198/jcgs.2009.07118
xCell	https://xcell.ucsf.edu/	
Xfuse	https://github.com/ludvb/xfuse	
ZIFA		https://doi.org/10.1186/s13059-015-0805-z
zinbwave	https://www.bioconductor.org/packages/release/bioc/html/zinbwave.html	https://doi.org/doi:10.18129/B9.bioc.zinbwave