Package	Download_score
a4	163
a4Base	186
a4Classif	157
a4Core	193
a4Preproc	185
a4Reporting	154
ABAEnrichment	36
ABarray	164
abseqR	109
ABSSeq	176
acde	131
ACE	138
aCGH	232
ACME	178
ADaCGH2	148
ADAM	196
ADAMgui	110
ADAPT	19
adaptest	12
adductomicsR	105
ADImpute	116
adSplit	150
adverSCarial	81
AffiXcan	104
affxparser	1561
affy	7722
affycomp	173
AffyCompatible	72
affyContam	169
affycoretools	400
AffyExpress	58
affyILM	151
affyio	7836
affylmGUI	173
affyPara	58
affypdnn	55
affyPLM	938
affyQCReport	63
AffyRNADegradation	135
AffyTiling	40
AGDEX	136
aggregateBioVar	112
Agi4x44PreProcess	20
agilp	151
AgiMicroRna	202
AHMassBank	89
AIMS	360
airpart	109
alabaster	95
alabaster.base	3144
alabaster.bumpy	99
alabaster.files	80
alabaster.mae	102
alabaster.matrix	3140
alabaster.ranges	3011
alabaster.sce	1024
alabaster.schemas	2811
alabaster.se	2931
alabaster.sfe	2
alabaster.spatial	103
alabaster.string	105
alabaster.vcf	102
ALDEx2	1210
alevinQC	128
AllelicImbalance	157
AlphaBeta	100
AlphaMissenseR	89
alpine	41
ALPS	11
AlpsNMR	124
alsace	40
altcdfenvs	160
AMARETTO	200
AMOUNTAIN	116
amplican	131
ampliQueso	34
AnalysisPageServer	29
anamiR	14
Anaquin	111
ANCOMBC	1240
AneuFinder	143
ANF	114
animalcules	251
annaffy	299
AnnBuilder	10
annmap	123
annotate	17001
AnnotationDbi	36310
AnnotationFilter	10788
AnnotationForge	1964
AnnotationFuncs	48
AnnotationHub	11440
AnnotationHubData	326
annotationTools	163
annotatr	465
anota	142
anota2seq	125
antiProfiles	129
AnVIL	506
AnVILAz	52
AnVILBase	128
AnVILBilling	91
AnVILGCP	57
AnVILPublish	102
AnVILWorkflow	83
APAlyzer	120
apComplex	147
apeglm	3680
APL	185
applera	2
appreci8R	107
aroma.light	1824
ArrayExpress	426
ArrayExpressHTS	49
arrayMagic	8
arrayMvout	140
arrayQCplot	2
arrayQuality	230
arrayQualityMetrics	463
ArrayTools	56
ArrayTV	40
ARRmNormalization	129
artMS	124
ASAFE	100
ASEB	126
ASGSCA	123
ASICS	138
asmn	6
ASpediaFI	20
ASpli	144
AssessORF	190
ASSET	157
ASSIGN	161
assorthead	4822
ASURAT	100
ATACCoGAPS	52
ATACseqQC	393
ATACseqTFEA	93
atena	101
AtlasRDF	24
atSNP	123
attract	152
AUCell	2571
autonomics	95
Autotuner	10
AWFisher	107
awst	96
BaalChIP	120
BAC	51
bacon	179
BADER	132
BadRegionFinder	112
BAGS	139
ballgown	555
bambu	299
bamsignals	963
BANDITS	124
bandle	97
Banksy	220
banocc	122
barcodetrackR	96
basecallQC	116
BaseSpaceR	138
Basic4Cseq	137
BASiCS	159
BASiCStan	119
BasicSTARRseq	109
basilisk	3288
basilisk.utils	3181
batchelor	3910
BatchQC	157
BayesKnockdown	106
BayesPeak	48
BayesSpace	286
bayNorm	130
baySeq	472
BBCAnalyzer	122
BCRANK	156
bcSeq	108
BDMMAcorrect	35
beachmat	15612
beachmat.hdf5	136
beachmat.tiledb	20
beadarray	652
beadarraySNP	75
BeadDataPackR	548
BeadExplorer	6
BEARscc	74
BEAT	130
BEclear	136
bedbaser	10
beer	98
benchdamic	99
BERT	75
betaHMM	72
betr	45
bettr	74
BG2	87
bgafun	51
BgeeCall	90
BgeeDB	160
BGmix	44
bgx	116
BHC	87
BicARE	166
BiFET	114
BiGGR	124
bigmelon	120
bigmemoryExtras	39
bigPint	28
bim	4
BindingSiteFinder	98
bioassayR	137
Biobase	49698
biobroom	257
biobtreeR	88
bioCancer	120
BioCartaImage	79
BiocBaseUtils	6708
BiocBook	99
BiocCaseStudies	57
BiocCheck	1629
biocDatasets	9
BiocDockerManager	16
BiocFHIR	89
BiocFileCache	25666
BiocGenerics	57536
biocGraph	267
BiocHail	52
BiocHubsShiny	121
BiocInstaller	210
BiocIO	19406
biocmake	14
BiocNeighbors	10842
BiocOncoTK	69
BioCor	123
BiocParallel	41773
BiocPkgTools	172
biocroxytest	82
BiocSet	352
BiocSingular	12633
BiocSklearn	132
BiocStyle	5400
biocthis	264
BiocVersion	60157
biocViews	4355
BiocWorkflowTools	201
biodb	144
biodbChebi	104
biodbExpasy	56
biodbHmdb	104
biodbKegg	69
biodbLipidmaps	35
biodbMirbase	16
biodbNcbi	90
biodbNci	98
biodbUniprot	90
bioDist	281
BioGA	51
biomaRt	21639
BioMedR	4
biomformat	5500
BioMM	21
BioMVCClass	150
biomvRCNS	136
BioNAR	111
BioNERO	260
BioNet	277
BioNetStat	68
BioQC	165
BioSeqClass	50
biosigner	136
Biostrings	48000
biosvd	41
BioTIP	116
biotmle	115
biovizBase	4984
BiRewire	211
birta	45
birte	26
biscuiteer	114
BiSeq	149
BitSeq	58
blacksheepr	112
blima	129
BLMA	119
BloodGen3Module	139
bluster	5587
bnbc	203
bnem	100
BOBaFIT	95
borealis	95
BPRMeth	128
BRAIN	182
brainflowprobes	37
brainImageR	5
BrainSABER	14
BrainStars	47
branchpointer	130
breakpointR	114
brendaDb	103
BREW3R.r	73
BRGenomics	68
bridge	56
BridgeDbR	131
broadSeq	53
BrowserViz	177
BrowserVizDemo	16
BSgenome	15352
BSgenomeForge	188
bsseq	1401
BubbleTree	133
BufferedMatrix	140
BufferedMatrixMethods	137
bugsigdbr	251
BulkSignalR	7
BUMHMM	133
bumphunter	2579
BumpyMatrix	415
BUS	140
BUScorrect	105
BUSpaRse	220
BUSseq	100
CaDrA	77
CAEN	87
CAFE	132
CAGEfightR	262
cageminer	103
CAGEr	286
CALIB	56
calm	83
CAMERA	476
CAMTHC	10
CaMutQC	75
canceR	144
cancerclass	355
CancerInSilico	30
CancerMutationAnalysis	49
CancerSubtypes	77
CAnD	37
caOmicsV	26
cardelino	101
Cardinal	262
CardinalIO	181
CARDspa	8
CARNIVAL	189
casper	123
CATALYST	570
Category	1508
categoryCompare	136
CatsCradle	47
CausalR	125
cbaf	116
CBEA	84
cBioPortalData	361
CBNplot	138
cbpManager	94
ccfindR	123
ccImpute	96
ccmap	132
CCPlotR	103
CCPROMISE	107
ccrepe	184
CDI	81
celaref	114
celda	780
CellaRepertorium	30
CellBarcode	107
cellbaseR	123
CellBench	164
cellGrowth	39
cellHTS	45
cellHTS2	176
CelliD	219
cellity	115
CellMapper	105
cellmigRation	89
CellMixS	118
CellNOptR	186
cellscape	96
CellScore	103
CellTrails	108
cellTree	27
cellxgenedp	122
CEMiTool	187
censcyt	97
Cepo	154
ceRNAnetsim	84
CeTF	118
CexoR	134
CFAssay	107
cfdnakit	90
cfDNAPro	119
cfTools	83
CGEN	131
CGHbase	383
CGHcall	359
cghMCR	161
CGHnormaliter	143
CGHregions	154
ChAMP	715
CHARGE	12
charm	56
ChemmineOB	326
ChemmineR	795
CHETAH	138
chevreulPlot	3
chevreulProcess	3
chevreulShiny	2
ChIC	23
Chicago	139
chihaya	167
chimera	49
chimeraviz	144
ChIPanalyser	114
ChIPComp	122
chipenrich	172
ChIPexoQual	115
ChIPpeakAnno	987
ChIPQC	375
ChIPseeker	1965
chipseq	605
ChIPseqR	163
ChIPSeqSpike	17
ChIPsim	154
ChIPXpress	114
chopsticks	155
chroGPS	48
chromDraw	122
ChromHeatMap	143
ChromoViz	7
chromPlot	227
ChromSCape	104
chromstaR	107
chromswitch	32
chromVAR	1182
CHRONOS	111
cicero	259
CIMICE	93
CINdex	114
circRNAprofiler	115
CircSeqAlignTk	84
cisPath	115
CiteFuse	120
ClassifyR	339
cleanUpdTSeq	135
CleanUpRNAseq	51
cleaver	244
clevRvis	96
clippda	144
clipper	151
cliProfiler	90
cliqueMS	133
Clomial	114
Clonality	55
clonotypeR	48
clst	134
clstutils	134
CluMSID	97
ClustAll	81
clustComp	118
clusterExperiment	315
ClusterFoldSimilarity	76
ClusterJudge	109
clusterProfiler	21022
clusterSeq	117
ClusterSignificance	108
clusterStab	159
clustifyr	189
ClustIRR	89
CMA	200
cmapR	441
CNAnorm	135
CNEr	3295
cn.farms	138
cn.mops	240
CNORdt	133
CNORfeeder	138
CNORfuzzy	140
CNORode	149
CNPBayes	24
CNTools	179
CNVfilteR	100
CNVgears	34
cnvGSA	138
CNViz	95
CNVMetrics	96
CNVPanelizer	124
CNVRanger	127
CNVrd2	131
CNVtools	44
cobindR	46
CoCiteStats	142
COCOA	123
codelink	162
CODEX	148
coexnet	22
CoGAPS	324
cogena	141
cogeqc	107
Cogito	94
coGPS	132
COHCAP	56
cola	162
comapr	95
combi	125
coMET	90
coMethDMR	107
compartmap	41
COMPASS	149
compcodeR	145
compEpiTools	127
CompGO	38
ComplexHeatmap	15930
CompoundDb	257
ComPrAn	91
compSPOT	74
conclus	10
concordexR	106
condcomp	6
condiments	134
CONFESS	123
consensus	99
ConsensusClusterPlus	2922
consensusDE	109
consensusOV	129
consensusSeekeR	124
consICA	177
CONSTANd	92
contiBAIT	44
conumee	213
convert	186
copa	142
COPDSexualDimorphism	5
copynumber	129
CopyNumber450k	24
CopyNumberPlots	148
CopywriteR	49
coRdon	209
CoRegFlux	7
CoRegNet	57
CoreGx	270
Cormotif	142
CorMut	41
coRNAi	41
corral	114
CORREP	56
coseq	184
CoSIA	75
cosmiq	200
cosmo	16
cosmoGUI	14
cosmosR	128
COSNet	121
COTAN	123
CountClust	26
countsimQC	287
covEB	106
CoverageView	126
covRNA	107
CPSM	5
cpvSNP	121
cqn	315
CRImage	155
CRISPRball	84
crisprBase	155
crisprBowtie	150
crisprBwa	86
crisprDesign	139
crisprScore	162
CRISPRseek	174
crisprseekplus	38
crisprShiny	75
CrispRVariants	138
crisprVerse	119
crisprViz	122
crlmm	293
CrossICC	4
crossmeta	140
CSAR	153
csaw	512
csdR	87
CSSP	41
CSSQ	94
ctc	289
CTdata	84
CTDquerier	107
CTexploreR	73
ctgGEM	11
cTRAP	116
ctsGE	112
CTSV	97
cummeRbund	267
CuratedAtlasQueryR	98
customCMPdb	108
customProDB	156
CVE	17
cyanoFilter	95
cycle	143
cydar	133
cypress	72
CytoDx	125
cytofast	12
cytofkit	34
CyTOFpower	58
cytofQC	97
CytoGLMM	103
cytoKernel	107
cytolib	2473
cytomapper	326
CytoMDS	74
cytoMEM	129
CytoML	447
CytoPipeline	104
CytoPipelineGUI	78
CytoTree	15
cytoviewer	128
dada2	2414
dagLogo	141
daMA	134
DAMEfinder	101
DaMiRseq	131
Damsel	62
dandelionR	11
DAPAR	165
dar	66
DART	137
DASC	2
DASiR	28
dasper	15
DAVIDQuery	31
DBChIP	50
dcanr	183
DCATS	103
dce	84
dcGSA	102
DChIPRep	29
ddCt	164
ddgraph	37
ddPCRclust	126
dearseq	232
debCAM	108
debrowser	155
DECIPHER	2795
deco	19
DEComplexDisease	23
decompTumor2Sig	140
DeconRNASeq	307
decontam	1625
decontX	271
deconvR	111
decoupleR	1246
DEDS	50
DeepBlueR	35
DeepPINCS	92
deepSNV	189
DeepTarget	52
DEFormats	252
DegCre	68
DegNorm	100
DEGraph	109
DEGreport	607
DEGseq	224
DelayedArray	42179
DelayedDataFrame	103
DelayedMatrixStats	15972
DelayedRandomArray	100
DelayedTensor	96
DELocal	109
deltaCaptureC	96
deltaGseg	120
DeMAND	102
DeMixT	130
demuxmix	258
demuxSNP	82
densvis	1299
DEP	583
DepecheR	114
DepInfeR	87
DeProViR	41
DEqMS	284
derfinder	507
derfinderHelper	504
derfinderPlot	157
DEScan2	112
DESeq	193
DESeq2	22048
DEsingle	284
DESpace	95
destiny	688
DEsubs	106
DEWSeq	103
DExMA	101
DEXSeq	1420
dexus	48
DFP	144
DFplyr	37
DIAlignR	60
DiffBind	1096
diffcoexp	176
diffcyt	451
DifferentialRegulation	96
diffGeneAnalysis	127
diffHic	166
DiffLogo	131
diffloop	36
diffuStats	118
diffUTR	82
diggit	119
Dino	96
dinoR	72
Director	82
dir.expiry	3269
DirichletMultinomial	4615
discordant	132
DiscoRhythm	117
distinct	248
dittoSeq	1352
divergence	94
dks	112
DMCFB	104
DMCHMM	105
DMRcaller	147
DMRcate	1092
DMRforPairs	53
DMRScan	92
dmrseq	209
DNABarcodeCompatibility	86
DNABarcodes	185
DNAcopy	4823
DNAcycP2	3
DNAfusion	91
DNaseR	8
DNAshapeR	133
domainsignatures	41
DominoEffect	106
dominoSignal	46
doppelgangR	205
DOQTL	30
Doscheda	113
DOSE	19714
doseR	104
doubletrouble	106
dpeak	26
drawProteins	205
dreamlet	114
DRIMSeq	295
DriverNet	118
DropletUtils	2420
drugTargetInteractions	99
DrugVsDisease	165
dSimer	13
DSS	763
dStruct	87
DTA	126
dualKS	54
Dune	86
DupChecker	25
DuplexDiscovereR	34
dupRadar	165
dyebias	149
DynDoc	1387
easier	130
EasyCellType	116
easylift	87
EasyqpcR	46
easyreporting	97
easyRNASeq	179
EBarrays	204
EBcoexpress	139
EBImage	2778
EBSEA	106
EBSeq	378
EBSeqHMM	55
ecolitk	155
EDASeq	1660
edd	19
EDDA	41
edge	155
edgeR	23631
EDIRquery	79
eds	382
eegc	50
EGAD	120
EGSEA	267
eiR	129
eisa	56
eisaR	145
ELBOW	38
ELMER	227
ELViS	3
EMDomics	141
EmpiricalBrownsMethod	140
ENCODExplorer	34
EnhancedVolcano	5264
enhancerHomologSearch	85
EnMCB	101
ENmix	313
EnrichDO	42
EnrichedHeatmap	597
EnrichmentBrowser	528
enrichplot	20208
enrichTF	40
enrichViewNet	89
ensembldb	9577
ensemblVEP	124
ENVISIONQuery	45
epialleleR	101
EpiCompare	64
epidecodeR	90
EpiDISH	671
epigenomix	134
epigraHMM	101
epihet	18
EpiMix	92
epimutacions	94
epiNEM	136
EpipwR	38
epiregulon	76
epiregulon.extra	77
epistack	93
epistasisGA	86
EpiTxDb	101
epivizr	172
epivizrChart	113
epivizrData	148
epivizrServer	141
epivizrStandalone	112
erccdashboard	145
erma	152
ERSSA	105
esATAC	130
escape	437
escheR	110
esetVis	115
eudysbiome	111
evaluomeR	105
EventPointer	122
EWCE	278
ExCluster	87
ExiMiR	135
exomeCopy	196
exomePeak	47
exomePeak2	82
exonmap	13
ExperimentHub	7652
ExperimentHubData	269
ExperimentSubset	113
explorase	44
ExploreModelMatrix	230
ExpressionAtlas	228
ExpressionView	52
exprExternal	2
externalVector	14
extraChIPs	121
fabia	211
facopy	24
factDesign	145
factR	94
faers	98
FamAgg	126
famat	98
farms	70
fastLiquidAssociation	126
FastqCleaner	124
fastreeR	113
fastseg	781
fbat	11
FCBF	43
fCCAC	109
fCI	116
fcoex	18
fcScan	109
fdrame	136
FEAST	156
FeatSeekR	81
fedup	92
FELLA	170
FEM	40
fenr	84
ffpe	141
fgga	90
FGNet	143
fgsea	19970
FilterFFPE	104
findIPs	75
FindIT2	97
FindMyFriends	32
FISHalyseR	113
fishpond	264
FitHiC	120
flagme	126
FLAMES	114
flipflop	36
flowAI	549
flowBeads	128
flowBin	130
flowcatchR	136
flowCHIC	128
flowCL	46
flowClean	243
flowClust	728
flowCore	2577
flowCut	153
flowCyBar	114
flowDensity	287
flowFit	38
flowFlowJo	22
flowFP	191
flowGate	116
flowGraph	86
flowMap	65
flowMatch	133
flowMeans	175
flowMerge	167
flowPeaks	202
flowPhyto	15
flowPloidy	108
flowPlots	120
flowQ	41
flowQB	42
FlowRepositoryR	33
FlowSOM	1030
flowSpecs	119
flowSpy	7
flowStats	463
flowTime	113
flowTrans	159
flowType	43
flowUtils	71
flowViz	940
flowVS	159
flowWorkspace	1107
fmcsR	263
fmrs	138
fobitools	101
focalCall	29
FoldGO	36
FourCSeq	34
FRASER	151
frenchFISH	82
FRGEpistasis	112
frma	174
frmaTools	140
FScanR	18
FunChIP	43
FunciSNP	44
funOmics	52
funtooNorm	111
FuseSOM	95
G4SNVHunter	28
GA4GHclient	118
GA4GHshiny	111
gaga	149
gage	835
gaggle	73
gaia	52
GAPGOM	18
GAprediction	97
garfield	102
GARS	110
GateFinder	107
gatom	94
gaucho	31
GBScleanR	118
gcapc	111
gcatest	132
gCMAP	44
gCMAPWeb	37
gCrisprTools	113
gcrma	1117
GCSConnection	10
GCSFilesystem	10
GCSscore	22
GDCRNATools	231
gDNAx	96
gDR	80
gDRcore	88
gDRimport	91
gDRstyle	88
gDRutils	94
GDSArray	237
gdsfmt	2089
GeDi	84
geecc	35
GEM	108
gemini	86
gemma.R	110
genArise	124
genbankr	67
gene2pathway	14
GeneAccord	22
GeneAnswers	59
geneAttribution	115
GeneBreak	121
geneClassifiers	102
GENE.E	31
GeneExpressionSignature	156
genefilter	11627
genefu	337
GeneGA	108
GeneGeneInteR	104
GeneGroupAnalysis	9
GeneMeta	164
GeneNetworkBuilder	144
GeneOverlap	619
geneplast	139
geneplotter	4572
GeneR	17
geneRecommender	139
GeneRegionScan	150
GeneRfold	6
geneRxCluster	136
GeneSelectMMD	145
GeneSelector	47
GENESIS	378
GeneSpring	13
GeneStructureTools	117
geNetClassifier	164
GeneticsBase	11
GeneticsDesign	48
GeneticsPed	158
GeneTonic	313
GeneTraffic	11
GeneTS	7
geneXtendeR	107
GENIE3	1319
genoCN	119
GenoGAM	24
genomation	671
GenomAutomorphism	83
GenomeBase	1
GenomeGraphs	60
GenomeInfoDb	55139
genomeIntervals	202
genomes	142
GenomicAlignments	22732
GenomicDataCommons	1006
GenomicDistributions	143
GenomicFeatures	17945
GenomicFiles	1138
genomicInstability	107
GenomicInteractionNodes	92
GenomicInteractions	408
GenomicOZone	116
GenomicPlot	110
GenomicRanges	44975
GenomicScores	623
GenomicSuperSignature	108
GenomicTuples	124
Genominator	51
genoset	54
genotypeeval	41
GenoView	15
genphen	22
GenProSeq	83
GenRank	15
GenVisR	302
GeoDiff	105
GEOexplorer	105
GEOfastq	115
GEOmetadb	276
geomeTriD	41
GeomxTools	384
GEOquery	9766
GEOsearch	16
GEOsubmission	139
GeoTcgaData	199
gep2pep	103
gespeR	90
getDEE2	97
geva	94
GEWIST	112
geyser	17
gff3Plotter	3
gg4way	80
GGBase	58
ggbio	1836
ggcyto	797
ggkegg	528
ggmanh	270
ggmsa	541
GGPA	88
ggsc	125
ggseqalign	51
ggspavis	222
GGtools	64
ggtree	22126
ggtreeDendro	97
ggtreeExtra	1117
ggtreeSpace	73
GIGSEA	93
ginmappeR	75
gINTomics	55
girafe	165
GISPA	38
GLAD	226
GladiaTOX	95
Glimma	1029
glmGamPoi	4865
glmSparseNet	222
GlobalAncova	978
globalSeq	109
globaltest	1763
GloScope	87
gmapR	170
GmicR	105
gmoviz	96
GMRP	109
GNET2	97
GNOSIS	89
goCluster	1
GOexpress	145
GOfuncR	336
GOFunction	47
GoogleGenomics	23
GOpro	154
goProfiles	168
GOSemSim	19087
goseq	1436
GOSim	97
goSorensen	99
goSTAG	116
GOstats	1397
GOsummaries	56
GOTHiC	138
goTools	143
GPA	95
gpart	22
gpls	260
gprege	40
gpuMagic	91
gQTLBase	34
gQTLstats	36
GrafGen	70
gramm4R	9
GRaNIE	135
granulator	154
graper	97
graph	19275
GraphAlignment	123
GraphAT	152
graphite	3152
GraphPAC	113
GRENITS	117
GreyListChIP	1000
GRmetrics	141
groHMM	115
GRridge	30
GSALightning	93
GSAR	159
GSCA	123
gscreend	102
GSEABase	8774
GSEABenchmarkeR	127
GSEAlm	154
GSEAmining	104
gsean	109
GSgalgoR	95
GSReg	124
GSRI	141
GSVA	7290
gtrellis	169
GUIDEseq	135
Guitar	188
Gviz	3240
GWAS.BAYES	100
gwascat	606
GWASTools	635
gwasurvivr	137
GWENA	250
gypsum	2744
h5mread	98
h5vc	153
hapFabia	133
Harman	176
HarmonizR	97
Harshlight	148
hca	98
HCABrowser	9
HCAExplorer	7
HCAMatrixBrowser	3
HCsnip	34
HDF5Array	14604
HDTD	103
hdxmsqc	58
heatmaps	291
Heatplus	480
HelloRanges	143
HELP	137
HEM	142
hermes	253
HERON	78
Herper	148
hexbin	50
HGC	100
hiAnnotator	137
HIBAG	167
HicAggR	71
HiCBricks	165
HiCcompare	248
HiCDCPlus	129
HiCDOC	102
HiCExperiment	163
HiContacts	153
HiCool	96
HiCParser	9
hicrep	12
hicVennDiagram	85
hierGWAS	122
hierinf	87
HilbertCurve	147
HilbertVis	208
HilbertVisGUI	95
HiLDA	106
hipathia	210
HIPPO	95
hiReadsProcessor	128
HIREewas	103
HiTC	199
hmdbQuery	123
HMMcopy	371
HoloFoodR	50
hoodscanR	115
hopach	315
HPAanalyze	184
hpar	286
HPAStainR	14
HPiP	97
HTqPCR	102
HTSanalyzeR	50
HTSeqGenie	61
htSeqTools	46
HTSFilter	232
HuBMAPR	37
HubPub	146
HumanTranscriptomeCompendium	52
hummingbird	90
HybridExpress	87
HybridMTest	166
hypeR	150
hyperdraw	153
hypergraph	187
iASeq	117
iasva	111
iBBiG	151
ibh	126
iBMQ	101
iCARE	173
Icens	416
icetea	101
iCheck	120
iChip	138
iClusterPlus	423
iCNV	111
iCOBRA	297
ideal	135
IdeoViz	135
idiogram	142
IdMappingAnalysis	42
IdMappingRetrieval	46
idpr	109
idr2d	96
IFAA	86
iFlow	7
iGC	119
IgGeneUsage	96
igvR	157
igvShiny	87
IHW	676
illuminaio	2763
ILoReg	98
imageHTS	64
IMAS	108
imcRtools	258
Imetagene	31
IMMAN	100
immApex	20
ImmuneSpaceR	44
immunoClust	124
immunogenViewer	49
immunotation	94
IMPCdata	103
ImpulseDE	13
ImpulseDE2	21
impute	10543
INDEED	83
iNETgrate	87
infercnv	1164
infinityFlow	118
Informeasure	91
InPAS	132
INPower	129
inSilicoDb	33
inSilicoMerging	36
INSPEcT	122
INTACT	82
InTAD	107
intansv	142
interacCircos	97
InteractionSet	1805
InteractiveComplexHeatmap	411
interactiveDisplay	154
interactiveDisplayBase	4764
InterCellar	110
IntEREst	108
InterMineR	95
IntOMICS	11
IntramiRExploreR	102
inveRsion	42
IONiseR	133
iontree	35
iPAC	117
iPath	82
ipdDb	187
IPO	216
IPPD	41
IRanges	54674
IRISFGM	20
IrisSpatialFeatures	5
ISAnalytics	78
iSEE	495
iSEEde	95
iSEEfier	81
iSEEhex	142
iSEEhub	182
iSEEindex	87
iSEEpathways	88
iSEEtree	76
iSEEu	154
iSeq	115
ISLET	95
iSNetwork	4
isobar	155
IsoBayes	81
IsoCorrectoR	129
IsoCorrectoRGUI	100
IsoformSwitchAnalyzeR	290
IsoGeneGUI	54
ISoLDE	89
isomiRs	162
iSPlot	5
ITALICS	136
iterativeBMA	140
iterativeBMAsurv	122
iterClust	38
iteremoval	20
IVAS	128
ivygapSE	107
IWTomics	124
jazzPanda	6
jmosaics	26
joda	46
JunctionSeq	22
karyoploteR	789
katdetectr	99
KBoost	81
KCsmart	141
kebabs	164
KEGGgraph	5248
KEGGlincs	116
keggorth	7
keggorthology	244
KEGGprofile	53
KEGGREST	36218
KEGGSOAP	22
kimod	16
KinSwingR	103
kissDE	108
kmcut	50
KnowSeq	107
knowYourCG	73
koinar	42
LACE	184
lapmix	116
LBE	223
ldblock	144
LEA	631
LedPred	100
lefser	546
lemur	107
les	136
levi	84
lfa	300
limma	34756
limmaGUI	156
limpa	1
limpca	75
LimROTS	6
LINC	14
LineagePulse	32
lineagespot	88
LinkHD	109
Linnorm	197
LinTInd	91
lionessR	107
lipidr	160
LiquidAssociation	134
lisaClust	170
lmdme	132
LMGene	54
LOBSTAHS	140
loci2path	113
logicFS	159
logitT	65
Logolas	14
lol	36
LOLA	249
LoomExperiment	621
LowMACA	39
LPE	148
LPEadj	73
lpNet	130
lpsymphony	891
LRBaseDbi	113
LRcell	92
lumi	1209
lute	70
LVSmiRNA	44
LymphoSeq	121
M3C	593
M3D	30
M3Drop	590
m6Aboost	88
maanova	74
Maaslin2	939
maaslin3	16
Macarron	131
macat	79
maCorrPlot	125
MACPET	19
MACSQuantifyR	81
MACSr	128
maDB	22
made4	304
MADSEQ	109
maftools	2486
MAGAR	122
MAGeCKFlute	342
magpie	82
magrene	89
MAI	101
maigesPack	82
MAIT	194
makecdfenv	217
makePlatformDesign	9
MANOR	147
manta	47
MantelCorr	117
MAPFX	75
mAPKL	41
maPredictDSC	127
mapscape	88
mariner	89
marr	97
marray	1785
martini	107
maser	160
maSigPro	338
maskBAD	132
MassArray	115
massiR	127
MassSpecWavelet	1672
MAST	2073
mastR	179
matchBox	111
matchprobes	11
MatrixGenerics	41563
MatrixQCvis	189
MatrixRider	115
matter	244
MaxContrastProjection	16
MBAmethyl	98
MBASED	122
MBCB	131
MBECS	108
mbkmeans	371
mbOmic	9
mBPCR	138
MBQN	103
mbQTL	77
MBttest	105
mcaGUI	50
MCbiclust	112
MCRestimate	53
mCSEA	140
mdgsa	33
mdp	102
mdqc	143
MDTS	97
MEAL	143
MeasurementError.cor	125
MEAT	100
MEB	96
MEDIPS	185
MEDME	129
megadepth	172
MEIGOR	139
Melissa	102
memes	251
MergeMaid	57
Mergeomics	118
MeSHDbi	249
meshes	188
meshr	166
MeSHSim	16
MesKit	122
messina	123
metaArray	58
Metab	131
metabCombiner	142
metabinR	81
MetaboAnnotation	272
MetaboCoreUtils	1740
MetaboDynamics	13
metabolomicsWorkbenchR	118
metabomxtr	117
MetaboSignal	156
metaCCA	136
MetaCyto	120
metagene	50
metagene2	119
metagenomeFeatures	30
metagenomeSeq	1573
metahdep	129
metaMS	222
MetaNeighbor	139
MetaPhOR	101
metapod	4667
metapone	94
metaSeq	132
metaseqR	42
metaseqR2	118
metavizr	25
MetaVolcanoR	55
metaX	13
MetCirc	124
MethCP	15
methimpute	109
methInheritSim	114
methodical	60
MethPed	108
MethReg	90
methrix	131
MethTargetedNGS	116
methVisual	46
methyAnalysis	50
MethylAid	146
methylCC	112
methylclock	196
methylGSA	162
methyLImp2	81
methylInheritance	110
methylKit	667
MethylMix	154
methylMnM	127
methylPipe	146
methylscaper	124
MethylSeekR	199
methylSig	121
methylumi	1491
methyvim	16
MetID	104
MetMashR	32
MetNet	105
mfa	139
Mfuzz	1388
MGFM	120
MGFR	107
MGnifyR	105
mgsa	172
mia	1423
miaSim	116
miaViz	317
MiChip	128
microbiome	1801
microbiomeDASim	91
microbiomeExplorer	111
microbiomeMarker	383
MicrobiomeProfiler	158
MicrobiotaProcess	507
microRNA	227
microSTASIS	86
MICSQTL	78
midasHLA	91
MIGSA	25
miloR	440
mimager	109
MIMOSA	50
mina	79
MineICA	138
minet	710
minfi	2309
MinimumDistance	155
MiPP	145
miQC	150
MIRA	117
MiRaGE	136
miRBaseConverter	168
miRcomp	122
mirIntegrator	124
MIRit	84
miRLAB	133
miRmine	52
miRNAmeConverter	116
miRNApath	125
miRNAtap	192
miRSM	107
miRsponge	11
miRspongeR	95
Mirsynergy	37
mirTarRnaSeq	105
missMethyl	1087
missRows	104
mist	5
mistyR	140
mitch	98
mitoClone2	110
mitoODE	38
mixOmics	2731
MLInterfaces	412
mlm4omics	5
MLP	179
MLSeq	182
MMAPPR2	25
MMDiff	31
MMDiff2	110
mmgmos	3
mmnet	30
MmPalateMiRNA	46
MMUPHin	185
mnem	134
moanin	204
mobileRNA	71
MobilityTransformR	64
MODA	110
ModCon	81
Modstrings	145
MOFA	10
MOFA2	552
MOGAMUN	94
mogsa	267
MoleculeExperiment	107
MOMA	101
monaLisa	199
monocle	3371
Moonlight2R	84
MoonlightR	128
MoPS	28
mosaics	225
mosbi	93
MOSClip	36
mosdef	190
MOSim	110
Motif2Site	91
motifbreakR	210
motifcounter	107
MotifDb	583
motifmatchr	1327
MotifPeeker	20
motifRG	44
motifStack	668
motifTestR	92
MotIV	60
MouseFM	186
MPAC	52
MPFE	104
mpra	120
MPRAnalyze	116
MQmetrics	17
mQTL.NMR	28
msa	1856
MSA2dist	129
MsBackendMassbank	112
MsBackendMetaboLights	43
MsBackendMgf	460
MsBackendMsp	371
MsBackendRawFileReader	99
MsBackendSql	107
MsCoreUtils	3506
MsDataHub	123
MSEADbi	6
MsExperiment	1329
MsFeatures	1365
msgbsR	105
MSGFgui	36
MSGFplus	36
msImpute	233
mslp	78
msmsEDA	283
msmsTests	282
MSnbase	3032
MSnID	317
mspms	20
MSPrep	179
msPurity	122
msqrob2	190
MsQuality	94
MSstats	521
MSstatsBig	83
MSstatsBioNet	10
MSstatsConvert	441
MSstatsLiP	115
MSstatsLOBD	92
MSstatsPTM	201
MSstatsQC	114
MSstatsQCgui	97
MSstatsSampleSize	23
MSstatsShiny	131
MSstatsTMT	271
MSstatsTMTPTM	6
MTseeker	6
MuData	103
Mulcom	140
MultiAssayExperiment	6214
MultiBaC	116
multiClust	139
multicrispr	101
MultiDataSet	1170
multiGSEA	171
multiHiCcompare	157
MultiMed	116
multiMiR	316
MultimodalExperiment	78
multiOmicsViz	44
MultiRNAflow	101
multiscan	133
multiSight	14
multistateQTL	69
multiWGCNA	122
multtest	11827
mumosa	110
MungeSumstats	924
muscat	539
muscle	385
musicatk	122
MutationalPatterns	313
MVCClass	157
mvGST	27
MWASTools	164
mygene	355
myvariant	136
mzID	2941
mzR	3162
NADfinder	111
NanoMethViz	130
NanoStringDiff	144
NanoStringNCTools	383
NanoStringQCPro	50
nanotatoR	33
NanoTube	121
NarrowPeaks	45
NBAMSeq	194
NBSplice	22
ncdfFlow	1058
ncGTW	172
NCIgraph	113
ncRNAtools	100
ndexr	111
neaGUI	24
nearBynding	92
Nebulosa	1223
NeighborNet	31
nem	64
nempi	96
NetActivity	87
netbenchmark	27
netbiov	58
netboost	91
netboxr	16
netDx	49
nethet	132
netOmics	23
NetPathMiner	114
netprioR	96
netReg	18
netresponse	143
NetSAM	159
netSmooth	114
networkBMA	52
netZooR	91
NeuCA	52
NewWave	115
NGScopy	28
ngsReports	117
nipalsMCIA	90
nnNorm	143
nnSVG	189
NOISeq	601
nondetects	64
NoRCE	98
normalize450K	101
NormalyzerDE	214
NormqPCR	213
normr	174
NPARC	114
npGSEA	126
NTW	121
nucleoSim	112
nucleR	159
nuCpos	97
nudge	43
nullranges	188
NuPoP	137
NxtIRFcore	14
occugene	123
OCplus	158
octad	94
ODER	9
odseq	110
OGRE	94
OGSA	26
oligo	1731
oligoClasses	1597
OLIN	156
OLINgui	142
omada	84
OmaDB	230
omicade4	207
OmicCircos	237
omicplotR	110
omicRexposome	114
OmicsLonDA	24
OmicsMarkeR	29
OmicsMLRepoR	34
OMICsPCA	109
omicsPrint	113
omicsViewer	92
Omixer	99
OmnipathR	736
ompBAM	135
omXplore	43
Onassis	22
oncomix	104
oncoscanR	98
OncoScore	114
OncoSimulR	125
oneChannelGUI	54
oneSENSE	31
onlineFDR	81
ontoCAT	37
ontoProc	234
ontoTools	19
openCyto	626
openPrimeR	173
openPrimeRui	59
OpenStats	86
OperaMate	17
oposSOM	156
oppar	116
oppti	93
optimalFlow	103
OPWeight	104
OrderedList	147
ORFhunteR	95
ORFik	195
OrganismDbi	2684
Organism.dplyr	404
orthogene	354
orthos	91
OSAT	151
Oscope	128
OSTA.data	3
OTUbase	133
OutlierD	53
OUTRIDER	206
OutSplice	86
OVESEG	113
PAA	131
packFinder	104
padma	102
PADOG	325
pageRank	89
PAIRADISE	138
paircompviz	125
pairedGSEA	74
pairkat	121
pairseqsim	3
pamr	20
pandaR	160
panelcn.mops	116
PAnnBuilder	49
PanomiR	98
panp	163
PANR	130
PanViz	48
PanVizGenerator	23
PAPi	41
pareg	59
parglms	113
parody	149
partCNV	76
PAST	98
Path2PPI	121
pathifier	137
pathlinkR	103
PathNet	136
PathoStat	187
pathprint	14
pathRender	142
pathVar	36
pathview	4524
pathwayPCA	117
PathwaySplice	13
PatientGeneSets	5
paxtoolsr	109
Pbase	31
pbcmc	10
pcaExplorer	384
pcaGoPromoter	38
pcaMethods	5065
PCAN	115
PCAtools	1218
pcot2	62
PCpheno	51
pcxn	54
PDATK	174
pdInfoBuilder	183
pdmclass	49
PeacoQC	257
peakPantheR	98
PECA	137
peco	95
Pedixplorer	72
pengls	81
PepSetTest	47
PepsNMR	142
pepStat	117
pepXMLTab	121
PERFect	33
periodicDNA	92
perturbatr	15
pfamAnalyzeR	260
PFP	12
PGA	31
pgca	90
PGSEA	90
pgUtils	13
pgxRpi	78
phantasus	214
phantasusLite	97
PharmacoGx	259
phemd	28
phenoDist	35
PhenoGeneRanker	75
phenomis	98
phenopath	131
phenoTest	161
PhenStat	125
philr	196
PhIPData	107
phosphonormalizer	90
PhosR	158
PhyloProfile	112
phyloseq	5454
Pi	48
piano	402
PICB	14
pickgene	120
PICS	159
Pigengene	139
PING	143
pint	40
pipeComp	100
pipeFrame	147
PIPETS	73
Pirat	47
PIUMA	75
pkgDepTools	73
planet	215
planttfhunter	106
plasmut	76
plateCore	45
plethy	53
plgem	162
plier	180
PloGO2	37
plotgardener	246
plotGrouper	93
PLPE	138
plrs	39
PLSDAbatch	93
plw	56
plyinteractions	89
plyranges	1109
plyxp	35
pmm	111
pmp	147
PoDCall	70
podkat	127
poem	6
pogos	141
polyester	127
Polyfit	35
PolySTest	45
Polytect	19
POMA	209
POST	17
PoTRA	15
PowerExplorer	13
powerTCR	312
POWSC	104
ppcseq	96
PPInfer	219
ppiStats	64
pqsfinder	159
prada	63
pram	105
prebs	128
preciseTAD	103
PrecisionTrialDrawer	18
PREDA	145
predictionet	45
preprocessCore	14212
primirTSS	99
PrInCE	101
Prize	28
proActiv	110
proBAMr	119
proBatch	28
PROcess	159
procoil	132
ProCoNA	34
proDA	253
proFIA	29
profileplyr	257
profileScoreDist	103
progeny	472
projectR	123
pRoloc	277
pRolocGUI	155
PROMISE	139
PRONE	41
PROPER	150
PROPS	102
Prostar	135
prot2D	31
proteasy	23
proteinProfiles	108
ProteoDisco	93
ProteomicsAnnotationHubData	30
ProteoMM	121
proteoQC	31
protGear	95
ProtGenerics	11282
PSEA	55
psichomics	113
PSICQUIC	52
PSMatch	2028
psygenet2r	99
ptairMS	85
PubScore	11
pulsedSilac	13
puma	169
PureCN	203
pvac	134
pvca	284
Pviz	127
pwalign	5656
PWMEnrich	217
pwOmics	159
pwrEWAS	25
qckitfastq	111
qcmetrics	143
QDNAseq	339
QFeatures	2584
qmtools	94
qpcrNorm	148
qpgraph	203
qPLEXanalyzer	101
qrqc	57
qsea	119
qsmooth	178
QSutils	171
qsvaR	183
QTLExperiment	85
Qtlizer	99
QUALIFIER	45
quantiseqr	545
quantro	268
quantsmooth	644
QuartPAC	89
QuasR	362
QuaternaryProd	113
QUBIC	163
qusage	412
qvalue	18901
R3CPET	108
r3Cseq	150
R453Plus1Toolbox	152
R4RNA	639
RadioGx	104
raer	76
RaggedExperiment	782
RAIDS	86
rain	155
rama	53
RamiGO	34
ramr	95
ramwas	129
RandomWalkRestartMH	48
randPack	129
randRotation	85
RankProd	284
RAREsim	82
RareVariantVis	122
Rariant	45
Rarr	182
rawDiag	79
rawrr	196
RbcBook1	205
Rbec	92
RBGL	9070
RBioFormats	257
RBioinf	147
rBiopaxParser	198
rBLAST	171
RBM	121
Rbowtie	459
Rbowtie2	273
rbsurv	153
Rbwa	95
Rcade	55
RCAS	152
RCASPAR	112
rcellminer	142
rCGH	147
Rchemcpp	36
RchyOptimyx	45
RcisTarget	1147
RCM	109
Rcollectl	51
Rcpi	175
RCSL	99
Rcwl	105
RcwlPipelines	109
RCX	100
RCy3	844
RCyjs	125
RCytoscape	36
RDAVIDWebService	65
Rdbi	17
RdbiPgSQL	12
rDGIdb	83
Rdisop	443
RDRToolbox	183
ReactomeContentService4R	94
ReactomeGraph4R	51
ReactomeGSA	252
ReactomePA	2794
readat	15
ReadqPCR	232
reb	52
REBET	100
rebook	169
receptLoss	89
reconsi	90
recount	380
recount3	296
recountmethylation	116
recoup	113
RedeR	307
RedisParam	85
REDseq	157
ReducedExperiment	18
RefNet	36
RefPlus	80
RegEnrich	108
regionalpcs	94
RegionalST	76
regioneR	1779
regioneReloaded	94
regionReport	180
regsplice	106
regutools	112
REMP	120
Repitools	311
ReportingTools	556
reposTools	2
RepViz	99
ReQON	62
ResidualMatrix	3759
RESOLVE	89
Resourcerer	22
restfulSE	132
retrofit	79
ReUseData	87
rexposome	134
rfaRm	93
Rfastp	182
rflowcyt	16
rfPred	127
rGADEM	373
RGalaxy	47
rGenomeTracks	92
Rgin	18
RGMQL	59
RgnTX	88
rgoslin	142
RGraph2js	111
Rgraphviz	9098
rGREAT	647
RGSEA	132
rgsepd	113
rhdf5	20752
rhdf5client	154
rhdf5filters	20140
Rhdf5lib	22897
rhinotypeR	37
Rhisat2	216
Rhtslib	23817
rHVDM	51
RiboCrypt	92
RiboDiPA	97
RiboProfiling	147
ribor	102
riboSeqR	132
ribosomeProfilingQC	123
rifi	87
rifiComparative	82
Rigraphlib	7
rigvf	1
RImmPort	88
Ringo	177
Rintact	8
RIPAT	28
RIPSeeker	50
Risa	197
RITAN	117
RIVER	107
RJMCMCNucleosomes	112
RLassoCox	93
RLMM	131
RLSeq	24
RMAGEML	10
Rmagpie	144
RMAPPER	15
RMassBank	172
rMAT	46
rmelting	102
RmiR	49
Rmmquant	105
rmspc	79
RNAAgeCalc	112
RNAdecay	90
rnaEditr	104
RNAinteract	91
RNAither	59
RNAmodR	110
RNAmodR.AlkAnilineSeq	99
RNAmodR.ML	101
RNAmodR.RiboMethSeq	105
RNAprobR	32
RNAsense	92
rnaseqcomp	123
RNAseqCovarImpute	78
rnaSeqMap	49
RNASeqPower	220
RNASeqR	15
RnaSeqSampleSize	150
RnBeads	310
Rnits	121
roar	130
roastgsa	81
ROC	1105
ROCpAI	87
RolDE	97
Roleswitch	42
Rolexa	33
rols	425
ROntoTools	199
ropls	1151
ROSeq	104
ROTS	239
RPA	143
rprimer	111
RProtoBufLib	2465
RpsiXML	61
rpx	339
Rqc	308
rqt	87
rqubic	150
rRDP	127
Rredland	8
RRHO	147
rrvgo	529
Rsamtools	23413
rsbml	175
rScudo	100
rsemmed	85
RSeqAn	129
rSFFreader	35
RSNPper	11
Rsubread	2121
RSVSim	133
rSWeeP	98
rTANDEM	45
RTCA	137
RTCGA	473
RTCGAToolbox	496
RTN	216
RTNduals	116
RTNsurvival	109
RTools4TB	7
RTopper	138
Rtpca	107
rtracklayer	20203
Rtreemix	146
rTRM	171
rTRMui	124
runibic	112
Ruuid	17
RUVcorr	121
RUVnormalize	127
RUVSeq	894
Rvisdiff	80
RVS	102
RWebServices	23
rWikiPathways	380
S4Arrays	40122
S4Vectors	55288
safe	618
SAGElyzer	7
sagenhaft	131
SAGx	62
SAIGEgds	141
samExploreR	15
sampleClassifier	111
SamSPECTRAL	184
sangeranalyseR	223
sangerseqR	795
SANTA	113
sapFinder	40
saps	15
SARC	80
sarks	95
saseR	63
satuRn	288
savR	42
SBGNview	191
sbgr	11
SBMLR	145
SC3	356
Scale4C	118
ScaledMatrix	12410
scAlign	20
scanMiR	111
scanMiRApp	94
scAnnotatR	203
SCAN.UPC	174
SCANVIS	108
SCArray	110
SCArray.sat	94
SCATE	23
scater	7016
scatterHatch	87
scBFA	103
SCBN	110
scBubbletree	96
scCB2	101
scClassifR	5
scClassify	151
sccomp	133
scDataviz	116
scDblFinder	1658
scDD	171
scDDboost	90
scde	420
scDesign3	105
scDiagnostics	43
scDotPlot	64
scds	485
SCFA	91
scFeatureFilter	101
scFeatures	91
scfind	13
scGPS	126
schex	167
scHOT	102
scider	86
scifer	92
ScISI	60
scMAGeCK	11
scmap	249
scMerge	493
scMET	86
scmeth	109
scMitoMut	72
scMultiSim	75
SCnorm	152
scone	153
Sconify	101
SCOPE	110
scoreInvHap	110
scoup	36
scp	245
scPCA	128
scPipe	131
scQTLtools	13
scran	4633
scrapper	54
scReClassify	102
scRecover	102
screenCounter	85
ScreenR	82
scRepertoire	623
scRNAseqApp	93
scruff	110
scry	293
scShapes	88
scsR	38
scTensor	106
scTGIF	199
scTHI	92
scTreeViz	97
scuttle	9109
scviR	78
SDAMS	109
seahtrue	45
sechm	200
segmenter	102
segmentSeq	149
selectKSigs	94
SELEX	128
SemDist	119
semisup	103
SemSim	5
SEPA	22
SEPIRA	31
seq2pathway	216
seqArchR	92
seqArchRplus	81
SeqArray	910
seqbias	65
seqCAT	115
seqCNA	59
seqcombo	98
SeqGate	99
SeqGSEA	237
seq.hotSPOT	75
seqLogo	3682
seqPattern	757
seqplots	40
seqsetvis	125
SeqSQC	198
seqTools	160
SeqVarTools	455
sesame	815
SEtools	208
sevenbridges	119
sevenC	101
SGCP	165
SGSeq	321
SharedObject	131
shinyepico	99
shiny.gosling	84
shinyMethyl	165
shinyTANDEM	37
ShortRead	6076
SIAMCAT	165
SICtools	106
sigaR	42
SigCheck	113
sigFeature	303
SigFuge	130
siggenes	3144
sights	113
signatureSearch	192
signeR	125
signet	11
signifinder	73
sigPathway	71
SigsPack	94
sigsquared	119
SIM	142
SIMAT	121
SimBindProfiles	64
SimBu	185
SIMD	101
SimFFPE	92
similaRpeak	122
SIMLR	206
simona	295
simPIC	72
simpleaffy	111
simpleSeg	103
simplifyEnrichment	989
simulatorAPMS	12
simulatorZ	34
sincell	123
single	42
SingleCellAlleleExperiment	87
SingleCellExperiment	16077
SingleCellSignalR	239
singleCellTK	346
SingleMoleculeFootprinting	103
SingleR	4279
singscore	1489
SiPSiC	87
SISPA	43
sitadela	92
sitePath	104
sizepower	135
SJava	20
sketchR	88
skewr	116
slalom	139
SLGI	62
slingshot	1541
slinky	18
SLqPCR	140
SMAD	93
SMAP	70
smartid	85
SMITE	104
smoothclust	80
smoppix	15
SNAGEE	126
snapCGH	86
snapcount	101
snifter	165
snm	170
SNPchip	57
SNPediaR	96
SNPhood	121
snpMatrix	14
SNPRelate	1695
snpStats	2056
soGGi	379
sojourner	19
SomatiCA	27
SomaticSignatures	200
SOMNiBUS	85
sosta	20
SpaceMarkers	72
SpacePAC	112
spade	30
Spaniel	118
SpaNorm	43
sparrow	367
SparseArray	41459
sparseDOSSA	36
sparseMatrixStats	15428
sparsenetgls	92
SparseSignatures	107
spaSim	95
SpatialCPie	121
spatialDE	134
SpatialDecon	226
SpatialExperiment	4755
SpatialExperimentIO	20
spatialFDA	19
SpatialFeatureExperiment	210
spatialHeatmap	226
SpatialOmicsOverlay	101
spatialSimGP	35
spatzie	85
speckle	254
specL	125
SpeCond	147
Spectra	1836
SpectralTAD	119
SpectraQL	40
SPEM	148
SPIA	579
SPIAT	157
spicyR	201
SpidermiR	42
spikeLI	120
spiky	88
spillR	77
spkTools	135
splatter	443
splicegear	53
spliceR	36
spliceSites	37
SpliceWiz	155
SplicingFactory	88
SplicingGraphs	151
SplineDV	23
splineTCDiffExpr	1
splineTimeR	123
SPLINTER	99
splots	210
SPONGE	102
spoon	75
SpotClean	127
SPOTlight	286
spotSegmentation	46
SpotSweeper	72
spqn	95
SPsimSeq	192
SQLDataFrame	100
SQUADD	56
squallms	47
sRACIPE	111
SRAdb	461
sRAP	44
SRGnet	18
srnadiff	90
sscore	70
sscu	103
sSeq	197
ssize	164
sSNAPPY	185
SSPA	115
ssPATHS	96
ssrch	96
ssviz	129
StabMap	37
stageR	211
stam	8
STAN	43
standR	169
staRank	87
StarBioTrek	38
Starr	49
STATegRa	127
Statial	108
statTarget	144
STdeconvolve	141
stepNorm	141
stepwiseCM	37
stJoincount	100
strandCheckR	106
Streamer	137
STRINGdb	1365
STROMA4	35
struct	167
Structstrings	130
structToolbox	153
StructuralVariantAnnotation	224
SubCellBarCode	105
subSeq	133
SUITOR	80
SummarizedBenchmark	36
SummarizedExperiment	40248
Summix	89
supersigs	178
supraHex	365
surfaltr	91
SurfR	66
survClust	51
survcomp	1339
survtype	100
Sushi	74
sva	7363
svaNUMT	92
SVAPLSseq	14
svaRetro	94
SVM2CRM	27
SVMDO	96
SVP	3
SWATH2stats	115
SwathXtend	107
swfdr	114
SwimR	33
switchBox	147
switchde	107
synapsis	85
synapter	183
synergyfinder	253
SynExtend	102
synlet	114
SynMut	98
syntenet	135
systemPipeR	1204
systemPipeShiny	106
systemPipeTools	97
tadar	88
TADCompare	120
tanggle	114
TAPseq	107
target	103
TargetDecoy	104
TargetScore	137
TargetSearch	140
TarSeqQC	39
TBSignatureProfiler	95
TCC	269
TCGAbiolinks	4660
TCGAbiolinksGUI	35
TCGAutils	677
TCseq	523
TDARACNE	52
TDbasedUFE	92
TDbasedUFEadv	92
TEKRABber	177
TENET	2
TENxIO	101
tenXplore	91
TEQC	153
terapadog	6
ternarynet	122
terraTCGAdata	100
TFARM	103
TFBSTools	3356
TFEA.ChIP	131
TFHAZ	102
TFutils	119
tidybulk	336
tidyCoverage	72
tidyFlowCore	53
tidyomics	97
tidysbml	40
tidySingleCellExperiment	239
tidySpatialExperiment	87
tidySummarizedExperiment	346
tidytof	49
tigre	149
TileDBArray	115
tilingArray	180
timecourse	156
timeOmics	127
timescape	113
TimeSeriesExperiment	21
TimiRGeN	29
TIN	117
TissueEnrich	253
TitanCNA	149
tkWidgets	1394
tLOH	89
TMixClust	128
TMSig	39
TNBC.CMS	32
TnT	84
TOAST	445
tofsims	22
tomoda	101
tomoseqr	87
TOP	82
ToPASeq	34
topconfects	187
topdownr	113
topGO	2731
ToxicoGx	109
TPP	161
TPP2D	100
tpSVG	71
tracktables	211
trackViewer	608
tradeSeq	566
TrajectoryGeometry	77
TrajectoryUtils	1899
transcriptogramer	108
transcriptR	120
transformGamPoi	112
transite	109
tRanslatome	220
transmogR	72
transomics2cytoscape	109
TransView	103
TraRe	11
traseR	125
Travel	4
traviz	69
TreeAndLeaf	153
treeclimbR	76
treeio	21853
treekoR	109
TreeSummarizedExperiment	2076
TREG	90
trena	33
TReNA	3
Trendy	107
TRESS	99
tricycle	242
TrIdent	17
triform	47
trigger	142
trio	170
triplex	142
tripr	89
tRNA	126
tRNAdbImport	117
tRNAscanImport	109
TRONCO	133
TSAR	71
TSCAN	617
tscR	17
tspair	55
TSRchitect	23
TSSi	42
ttgsea	92
TTMap	107
TurboNorm	136
TVTB	109
tweeDEseq	185
twilight	161
twoddpcr	107
txcutr	90
txdbmaker	3753
tximeta	998
tximport	3432
TxRegInfra	15
TypeInfo	101
UCell	1539
UCSC.utils	34503
Ularcirc	105
UMI4Cats	94
uncoverappLib	96
UNDO	124
unifiedWMWqPCR	93
UniProt.ws	472
Uniquorn	112
universalmotif	914
updateObject	84
UPDhmm	66
uSORT	115
VAExprs	85
VanillaICE	252
VarCon	90
variancePartition	928
VariantAnnotation	11314
VariantExperiment	81
VariantFiltering	143
VariantTools	176
vasp	6
VaSP	99
vbmp	163
VCFArray	102
VDJdive	98
Vega	39
VegaMC	129
velociraptor	182
veloviz	87
VennDetail	299
VERSO	90
vidger	156
viper	732
virtualArray	13
ViSEAGO	143
VisiumIO	87
visiumStitched	19
vissE	144
Voyager	205
VplotR	106
vsclust	90
vsn	4888
vtpnet	134
vulcan	105
waddR	84
wateRmelon	859
wavClusteR	124
waveTiling	44
weaver	138
webbioc	145
weitrix	101
widgetInvoke	6
widgetTools	1390
wiggleplotr	180
wpm	105
wppi	77
Wrench	1567
XAItest	1
XBSeq	31
xCell2	17
XCIR	11
xcms	1578
xcore	87
XDE	155
XeniumIO	11
xenLite	40
Xeva	163
XINA	99
xmapbridge	119
xmapcore	8
XNAString	96
xps	46
XVector	49672
y2hStat	2
yamss	114
YAPSA	132
yaqcaffy	51
yarn	145
zellkonverter	1553
zenith	134
zFPKM	165
zinbwave	832
zitools	39
zlibbioc	53715
ZygosityPredictor	81