orginal name	standarized name
3uss	3USS
adapts	ADAPTS
affy	affy
altanalyze	AltAnalyze
annovar	ANNOVAR
apatrap	APAtrap
apriori	Apriori
asap	ASAP
backspin	BackSPIN
backspin2	BackSPIN
basic local alignment search tool	BLAST
bayesian regression for isoform estimation	BRIE
bayesian variable selection conditional logistic regression	BVS-CLR
bayesspace	BayesSpace
bbrowser	BBrowser
bcconf	BCconf
bcl2fastq	bcl2fastq
bedtools	BEDTools
biojupies	BioJupies
bionj	BIONJ
bioturing single cell browser	BBrowser
bismark	bismark
boosting weighted l2 loss	WL2Boost
bowtie	Bowtie
bowtie2	Bowtie
brie	BRIE
bseq - sc	bseqsc
bumphunter	bumphunter
bustools	bustools
bvs - clr	BVS-CLR
bwa	BWA
cate	cate
cell ranger	Cell Ranger
cell2location	cell2location
cellmarker	CellMarker
cellphonedb	CellPhoneDB
cellranger	Cell Ranger
celltalker	celltalker
cellxgene	cellxgene
champ	ChAMP
changepoint	changepoint
chromvar	chromVAR
cibersort	CIBERSORT
cidr	CIDR
cite - seq - counter	CITE-seq-counter
cite - seq - counter software	CITE-seq-counter
cite - seq counter	CITE-seq-counter
clarans	CLARANS
clusterprofiler	Cluster
clustvis	ClustVis
co - expression tables analysis	COTAN
combat	ComBat
combat - seq	ComBat
comet	COMET
comics	ComICS
consensusclusterplus	ConsensusClusterPlust
corrconf	CorrConf
cotan	COTAN
cssam	csSAM
cufflinks	Cufflinks
cutadapt	Cutadapt
cytobank	Cytobank
cytoscape	Cytoscape
dampened weighted least squares	DWLS
dapars	DaPars
database for annotation , visualization and integrated discovery	DAVID
david	DAVID
david bioinformatics resources	DAVID
dbscan	dbscan
dcq	ComICS
ddrtree	DDRTree
deconrna - seq	DeconRNASeq
desc	desc
deseq	DESeq2
deseq2	DESeq2
desingle	Desingle
diffusion pseudotime	DPT
divo	divo
dnamtl	DNAmtl
dpt	DPT
dsva	dSVA
dwls	DWLS
edger	edgeR
enrichplot	enrichplot
enrichr	Enrichr
estimate	ESTIMATE
fastproject	FastProject
fastqc	FastQC
featurecounts	featureCounts
fimo	FIMO
flowjo	FlowJo
flowjo ™	FlowJo
fp	FastProject
fvfc	FVFC
g : profiler	g:Profiler
gatk	GATK
gear	gEAR
gene expression analysis resource	gEAR
gene multiple association network integration algorithm	GeneMANIA
gene set enrichment analysis	gsea
gene set variation analysis	GSVA
genefu	genefu
genehancer	GeneHancer
genemania	GeneMANIA
genepattern	GenePattern
genome analysis toolkit	GATK
genomicalignments	GenomicAlignments
geoquery	GEOQuery
gephi	Gephi
ggfortify	ggfortify
ggplot2	ggplot2
ggpubr	ggpubr
ggsashimi	ggsashimi
giotto	Giotto
gistic	GISTIC
gorilla	GOrilla
gpfates	Gpfates
gprofiler	g:Profiler
granatum	Granatum
graph pad	GraphPad Prism
graphpad	GraphPad Prism
graphpad prism	GraphPad Prism
graphpad prism8	GraphPad Prism
gsea	gsea
gsea ( gene set enrichment analysis	gsea
gsva	GSVA
harmony	Harmony
heatmap.2	heatmap
hisat2	HISAT2
histocat	Histocat
homer	HOMER
htseq	HTSeq
icellr	iCellR
igv	igv
imagej	ImageJ
integrative genome browser	igv
integrative genomics viewer	Integrative Genomics Viewer
internal spike - in - like - genes normalization	ISnorm
intmap	IntMAP
ion torrent mapping alignment program	IntMAP
isee	iSEE
isnorm	ISnorm
isoform - patterns	ISOP
isomap	isomap
isop	ISOP
jmp	JMP
jvenn	jvenn
kallisto	Kallisto
kraken	Kraken
liayson	liayson
lifelines	lifelines
liger	Liger
limma	limma
lle	lle
lmqcm	lmQCM
local maximal quasi - clique merger	lmQCM
loom - viewer	loom-viewer
loupe cell browser	Loupe Browser
lumi	lumi
macs2	MACS
maftools	maftools
estimation of stromal and immune cells in malignant tumors using expression data	ESTIMATE
mandalorion	Mandalorion
mapper	Mapper
mast	MAST
matrixeqtl	MatrixEQTL
max - relevance - max - distance	MRMD
metascape	Metascape
mfa	MFA
millefy	millefy
minfi	minfi
minimum - redundancy - maximum - relevancy	mRMR
miso	MISO
misty	MISTy
mixture - of - isoforms	MISO
mixture of isoforms	MISO
mixtures of factor analysers	MFA
mnncorrect	mnnCorrect
model - based analysis of single - cell transcriptomics	MAST
monocle	Monocle
monocle2	Monocle
monocle3	Monocle
monocle5	Monocle
morpheus	Morpheus
mousenet	MouseNetV2
mpath	mpath
mrmd	MRMD
mrmr	mRMR
music	MUSIC
mutect2	MuTect
oncoprint	Oncoprint
p - hipster	p-hipster
pagoda2	PAGODA
pamr	pamr
panglao	PanglaoDB
panglaodb	PanglaoDB
pathway level analysis of gene expression	PLAGE
pheatmap	pheatmap
phenoageaccel	PhenoAgeAccel 
phenograph	PhenoGraph
phenotest	phenoTest
picard	Picard
pisa	PISA
plage	PLAGE
polyester	Polyester
pql	PQL
pqlboost	PQL
prcomp	prcomp
prediction analysis for microarrays	Prediction Analysis for Microarrays (PAM)
prism	GraphPad Prism
prism	GraphPad Prism
prism ( graphpad )	GraphPad Prism
prism7	GraphPad Prism
profvis	profvis
pseudogp	pseudogp
raceid	RaceID
raceid3	RaceID
random penalized conditional logistic regression	RPCLR
rbpdb	RBPDB
rctd	RCTD
retnet	RetNet
rna - seqc	RNASeQC
rp - clr	RPCLR
rp - clu	RPCLR
rpclr	RPCLR
rsem	RSEM
rsem-1.3.0	RSEM
rsubread	Rsubread
rtsne	t-SNE
ruv	RUVSeq
safe	safe
sam tools	SAMtools
sambamba	Sambamba
samtools	SAMtools
saver	SAVER
sc3	SC3
scanpy	scanpy
scapa	scAPAmod
scda	scDA
scdapa	scDAPA
scdeepcluster	scDeppCluster
scdesk	scziDesk
sceasy	sceasy
scegmm	scEntropy
scenic	SCENIC
scid	scID
scimpute	scImpute
sclvm	scLVM
scmappr	scMapper
scmerge	scMerge
scmerge_supervised	scMerge
scnorm	SCnorm
scone	scone
scope	Scope
scran	scran
scsdaes	scSDAE
scsva	scSVA
sctransform	sctransform
scvae	scVAE
scvi	not_disambiguated
sczidesk	scziDesk
search tool for the retrieval of interacting genes	STRING
seurat	Seurat
seurat58	Seurat
shallow sparsely - connected autoencoders	SSCA
shallow sparsely - connected variational autoencoders	SSCA
sierra	Sierra
signac	Signac
simlr	SIMLR
single - cell mapper	scMapper
single - cell signature explorer	Single Cell Signature Explorer
single - cell virtual cytometer	Single Cell Virtual Cytometer
single - sample gene set enrichment analysis	ssGSEA
single cell discriminant analysis	scDA
single cell explorer	cellxgene
single cell mapper	scMapper
single‐cell regulatory network inference and clustering	SCENIC
singler	SingleR
singler2	SingleR
singlesplice	SingleSplice
slice	not_disambiguated
slicer	3D Slicer
slingshot	Slingshot
smile	SMILE
soup	SOUP
spacell	SpaCell
spade	SPAdes
spagcn	SpaGCN
spaotsc	SpaOTsc
spark	SPARK
sparsedc	SparseDC
sparsely - connected autoencoders	SSCA
spatialde	SpatialDE
spatialdwls	SpatialDWLS
splatter	Splatter
splotch	Splotch
spotlight	SPOTlight
spring	SPRING
squidpy	squidpy
ssca	SSCA
sscas	SSCA
sscva	SSCA
sscvas	SSCA
ssgsea	ssGSEA
star	STAR
star-2.5.2a	STAR
star-fusion	Star-Fusion
starsolo	StarSolo
startrac	STARTRAC
stereoscope	Stereoscope
stlearn	stLearn
string	STRING
stutility	STUtility
subread	Subread
survival	survival
survminer	survminer
sva	sva
t - distributed stochastic neighbor embedding	t-SNE
t - sne	t-SNE
t - stochastic neighbor embedding	t-SNE
t - stochastic neighborhood embedding	t-SNE
t‐distributed stochastic neighbor embedding	t-SNE
t‐distributed stochastic neighborhood embedding	t-SNE
t‐sne	t-SNE
t‐sne ( t‐distributed stochastic neighbor embedding	t-SNE
t‐stochastic neighbor embedding	t-SNE
tangram	Tangram
targetscan	TargetScan
tectool	TECtool
tmap	TMAP
toppgene	Toppgene
topslam	Topslam
tracer	Tracer
trendsceek	Trendsceek
trim galore	Trim Galore
trim galore !	Trim Galore
trimmomatic	Trimmomatic
tscan	TSCAN
tsne	t-SNE
ucsc cell browser	UCSC genome browser
ucsc genome browser	UCSC genome browser
umap	UMAP
uniform manifold approximation and projection	UMAP
uniform manifold approximation and projection algorithm	UMAP
universalmotif	universalmotif
university of california santa cruz ( ucsc ) genome browser	UCSC genome browser
upset	UpSet
valerie	VALERIE
velocyto	Velocyto
viper	viper
viral - track	Viral-Track
visualizing alternative splicing events in single - cell ribonucleic acid	VALERIE
visualizing alternative splicing events in single - cell ribonucleic acid ( rna ) -sequencing experiments	VALERIE
wanderlust	Wanderlust
waterfall	Waterfall
weighted correlation network analysis	WGCNA
weighted gene co - correlation network analysis	WGCNA
weighted gene co - expression network analysis	WGCNA
wemiq	WemIQ
wgcna	WGCNA
wgcna weighted gene coexpression network analysis	WGCNA
whole gene network correlation analysis	WGCNA
whole genome correlation network analysis	WGCNA
wishbone	Wishbone
wishbone3	Wishbone
wl2boost	PQL
wl2boot	PQL
xcell	xCell
xfuse	Xfuse
zero inflated factor analysis	ZIFA
zifa	ZIFA
zinbwave	zinbwave
zinbwave_normalized	zinbwave
