See download stats for: Bioconductor annotation packages Bioconductor experiment packages Bioconductor workflow packages

Download stats for Bioconductor software packages

Data as of Sat. 03 May 2025.

The number reported next to each package name is the download score, that is, the average number of distinct IPs that "hit" the package each month for the last 12 months (not counting the current month).

Top 75


1	BiocVersion (60847)	26	GenomicAlignments (22633)	51	preprocessCore (14353)
2	BiocGenerics (58191)	27	ggtree (22433)	52	BiocSingular (12687)
3	S4Vectors (55762)	28	treeio (22424)	53	ScaledMatrix (12444)
4	IRanges (55450)	29	DESeq2 (21960)	54	multtest (11783)
5	GenomeInfoDb (55129)	30	biomaRt (21480)	55	genefilter (11540)
6	zlibbioc (52371)	31	clusterProfiler (21429)	56	ProtGenerics (11243)
7	Biobase (50428)	32	rhdf5 (21017)	57	VariantAnnotation (11186)
8	XVector (50265)	33	fgsea (20977)	58	AnnotationHub (11106)
9	Biostrings (48051)	34	DOSE (20734)	59	BiocNeighbors (10892)
10	GenomicRanges (45414)	35	enrichplot (20654)	60	AnnotationFilter (10782)
11	BiocParallel (44021)	36	rhdf5filters (20613)	61	impute (10571)
12	DelayedArray (42710)	37	rtracklayer (20143)	62	GEOquery (9882)
13	SparseArray (42526)	38	graph (19396)	63	ensembldb (9527)
14	MatrixGenerics (42243)	39	BiocIO (19379)	64	scuttle (9098)
15	SummarizedExperiment (40868)	40	GOSemSim (19378)	65	Rgraphviz (9032)
16	S4Arrays (40396)	41	qvalue (19255)	66	RBGL (8969)
17	UCSC.utils (37967)	42	GenomicFeatures (17545)	67	GSEABase (8736)
18	AnnotationDbi (36761)	43	annotate (16955)	68	affyio (7785)
19	KEGGREST (36631)	44	SingleCellExperiment (16257)	69	affy (7665)
20	limma (35180)	45	ComplexHeatmap (16163)	70	ExperimentHub (7639)
21	BiocFileCache (25022)	46	DelayedMatrixStats (15983)	71	sva (7365)
22	Rhtslib (23738)	47	beachmat (15565)	72	GSVA (7270)
23	edgeR (23701)	48	sparseMatrixStats (15413)	73	scater (7107)
24	Rsamtools (23411)	49	BSgenome (15153)	74	BiocBaseUtils (6715)
25	Rhdf5lib (22946)	50	HDF5Array (14682)	75	pwalign (6295)

All software packages

All software package stats in one file: bioc_pkg_stats.tab

All software download scores in one file: bioc_pkg_scores.tab

See Download stats for Bioconductor software repository (all packages combined)

A

a4Classif (152)

a4Preproc (179)

a4Reporting (150)

ABAEnrichment (37)

adductomicsR (113)

adverSCarial (88)

affxparser (1584)

AffyCompatible (69)

affyContam (165)

affycoretools (397)

AffyExpress (53)

affylmGUI (172)

affyQCReport (58)

AffyRNADegradation (136)

AffyTiling (39)

aggregateBioVar (120)

Agi4x44PreProcess (22)

AgiMicroRna (207)

AHMassBank (90)

alabaster (102)

alabaster.base (3394)

alabaster.bumpy (102)

alabaster.files (83)

alabaster.mae (103)

alabaster.matrix (3397)

alabaster.ranges (3268)

alabaster.sce (1112)

alabaster.schemas (3054)

alabaster.se (3185)

alabaster.sfe (10)

alabaster.spatial (107)

alabaster.string (102)

alabaster.vcf (104)

AllelicImbalance (150)

AlphaBeta (109)

AlphaMissenseR (98)

altcdfenvs (154)

AMOUNTAIN (124)

ampliQueso (32)

AnalysisPageServer (30)

AneuFinder (148)

animalcules (255)

AnnBuilder (11)

annotate (16955)

AnnotationDbi (36761)

AnnotationFilter (10782)

AnnotationForge (1865)

AnnotationFuncs (42)

AnnotationHub (11106)

AnnotationHubData (304)

annotationTools (162)

anota2seq (132)

antiProfiles (131)

AnVILBase (165)

AnVILBilling (98)

AnVILPublish (106)

AnVILWorkflow (89)

apComplex (148)

appreci8R (109)

aroma.light (1776)

ArrayExpress (421)

ArrayExpressHTS (45)

arrayMvout (138)

arrayQCplot (3)

arrayQuality (236)

arrayQualityMetrics (454)

ArrayTools (51)

ARRmNormalization (133)

AssessORF (199)

assorthead (5895)

ATACCoGAPS (44)

ATACseqQC (389)

ATACseqTFEA (95)

autonomics (106)

B

BadRegionFinder (112)

bamsignals (931)

barcodetrackR (106)

basecallQC (123)

BaseSpaceR (139)

Basic4Cseq (136)

BASiCStan (122)

BasicSTARRseq (112)

basilisk (3277)

basilisk.utils (3176)

batchelor (3948)

BayesKnockdown (110)

BayesSpace (296)

BBCAnalyzer (128)

BDMMAcorrect (32)

beachmat (15565)

beachmat.hdf5 (145)

beachmat.tiledb (29)

beadarray (646)

beadarraySNP (69)

BeadDataPackR (537)

BeadExplorer (7)

benchdamic (102)

bigmemoryExtras (35)

BindingSiteFinder (105)

bioassayR (133)

Biobase (50428)

bioCancer (122)

BioCartaImage (88)

BiocBaseUtils (6715)

BiocCaseStudies (53)

BiocCheck (1573)

biocDatasets (9)

BiocDockerManager (15)

BiocFileCache (25022)

BiocGenerics (58191)

biocGraph (269)

BiocHubsShiny (126)

BiocInstaller (174)

BiocNeighbors (10892)

BiocOncoTK (65)

BiocParallel (44021)

BiocPkgTools (184)

biocroxytest (90)

BiocSingular (12687)

BiocSklearn (144)

BiocStyle (5435)

BiocVersion (60847)

biocViews (4318)

BiocWorkflowTools (202)

biodbChebi (108)

biodbExpasy (51)

biodbHmdb (111)

biodbLipidmaps (31)

biodbMirbase (14)

biodbUniprot (96)

biomaRt (21480)

biomformat (5562)

BioMVCClass (150)

biomvRCNS (131)

BioNetStat (60)

BioSeqClass (49)

biosigner (140)

Biostrings (48051)

biovizBase (4937)

biscuiteer (115)

blacksheepr (119)

BloodGen3Module (146)

brainflowprobes (31)

brainImageR (6)

BrainSABER (16)

BrainStars (40)

branchpointer (136)

breakpointR (118)

BreastSubtypeR (8)

BRGenomics (54)

BridgeDbR (139)

BrowserViz (176)

BrowserVizDemo (15)

BSgenome (15153)

BSgenomeForge (194)

BubbleTree (143)

BufferedMatrix (141)

BufferedMatrixMethods (136)

bugsigdbr (306)

BulkSignalR (15)

bumphunter (2496)

BumpyMatrix (370)

BUScorrect (113)

C

CAGEfightR (269)

cageminer (104)

cancerclass (378)

CancerInSilico (30)

CancerMutationAnalysis (46)

CancerSubtypes (75)

cardelino (104)

CardinalIO (187)

Category (1395)

categoryCompare (134)

CatsCradle (57)

cBioPortalData (355)

cbpManager (103)

CCPROMISE (111)

CellaRepertorium (28)

CellBarcode (114)

cellbaseR (124)

CellBench (169)

cellGrowth (34)

CellMapper (109)

cellmigRation (99)

CellNOptR (165)

cellscape (102)

CellScore (111)

CellTrails (117)

cellxgenedp (124)

ceRNAnetsim (92)

CGHnormaliter (144)

CGHregions (150)

ChemmineOB (326)

ChemmineR (789)

chevreulPlot (10)

chevreulProcess (10)

chevreulShiny (9)

chimeraviz (145)

ChIPanalyser (120)

chipenrich (169)

ChIPexoQual (115)

ChIPpeakAnno (933)

ChIPseeker (1964)

ChIPSeqSpike (18)

ChIPXpress (113)

chopsticks (157)

chromDraw (129)

ChromHeatMap (145)

chromPlot (235)

ChromSCape (112)

chromstaR (102)

chromswitch (34)

chromVAR (1173)

circRNAprofiler (116)

CircSeqAlignTk (85)

ClassifyR (337)

cleanUpdTSeq (137)

CleanUpRNAseq (61)

cliProfiler (96)

clonotypeR (40)

clstutils (139)

clustComp (123)

clusterExperiment (316)

ClusterFoldSimilarity (87)

ClusterJudge (116)

clusterProfiler (21429)

clusterSeq (122)

ClusterSignificance (117)

clusterStab (159)

clustifyr (197)

clustSIGNAL (8)

CNORfeeder (136)

CNORfuzzy (137)

CNVMetrics (103)

CNVPanelizer (126)

CNVRanger (134)

CoCiteStats (142)

coMethDMR (112)

compartmap (39)

compcodeR (149)

compEpiTools (129)

ComplexHeatmap (16163)

CompoundDb (257)

concordexR (113)

condiments (137)

consensus (107)

ConsensusClusterPlus (2893)

consensusDE (107)

consensusOV (123)

consensusSeekeR (124)

COPDSexualDimorphism (5)

copynumber (123)

CopyNumber450k (21)

CopyNumberPlots (137)

CopywriteR (45)

CountClust (26)

countsimQC (295)

CoverageView (132)

CRISPRball (94)

crisprBase (150)

crisprBowtie (139)

crisprDesign (135)

crisprScore (153)

CRISPRseek (163)

crisprseekplus (34)

crisprShiny (83)

CrispRVariants (145)

crisprVerse (121)

crisprViz (119)

crossmeta (116)

CTDquerier (115)

CTexploreR (82)

cummeRbund (265)

CuratedAtlasQueryR (104)

customCMPdb (112)

customProDB (148)

cyanoFilter (98)

CyTOFpower (52)

cytoKernel (114)

cytomapper (317)

CytoPipeline (110)

CytoPipelineGUI (86)

cytoviewer (130)

D

DAMEfinder (107)

dandelionR (21)

DAVIDQuery (30)

ddPCRclust (131)

debrowser (154)

DECIPHER (2797)

DEComplexDisease (26)

decompTumor2Sig (134)

DeconRNASeq (320)

decontam (1625)

DeconvoBuddies (9)

decoupleR (1301)

DeepTarget (61)

DEFormats (249)

DEGreport (603)

DelayedArray (42710)

DelayedDataFrame (104)

DelayedMatrixStats (15983)

DelayedRandomArray (103)

DelayedTensor (104)

deltaCaptureC (100)

deltaGseg (122)

derfinder (488)

derfinderHelper (484)

derfinderPlot (153)

DiffBind (1076)

diffcoexp (167)

DifferentialRegulation (102)

diffGeneAnalysis (127)

diffuStats (127)

dir.expiry (3284)

DirichletMultinomial (4510)

discordant (137)

DiscoRhythm (125)

dittoSeq (1317)

divergence (103)

DMRcaller (154)

DMRforPairs (51)

DNABarcodeCompatibility (92)

DNABarcodes (194)

DNAshapeR (143)

domainsignatures (38)

DominoEffect (107)

dominoSignal (55)

doppelgangR (206)

doubletrouble (111)

drawProteins (213)

DriverNet (121)

DropletUtils (2398)

drugTargetInteractions (105)

DrugVsDisease (146)

DupChecker (24)

DuplexDiscovereR (44)

E

EasyCellType (121)

easyreporting (105)

easyRNASeq (174)

EBcoexpress (143)

EmpiricalBrownsMethod (138)

ENCODExplorer (35)

EnhancedVolcano (5488)

enhancerHomologSearch (87)

EnrichedHeatmap (601)

EnrichmentBrowser (522)

enrichplot (20654)

enrichViewNet (92)

ensembldb (9527)

ensemblVEP (103)

ENVISIONQuery (40)

epialleleR (108)

EpiCompare (66)

epidecodeR (98)

epigenomix (134)

epigraHMM (105)

epimutacions (95)

epiregulon (84)

epiregulon.extra (88)

epistasisGA (94)

epivizrChart (116)

epivizrData (123)

epivizrServer (115)

epivizrStandalone (107)

erccdashboard (154)

eudysbiome (121)

evaluomeR (109)

EventPointer (127)

exomeCopy (153)

exomePeak2 (78)

ExperimentHub (7639)

ExperimentHubData (260)

ExperimentSubset (116)

ExploreModelMatrix (240)

ExpressionAtlas (232)

ExpressionView (49)

exprExternal (2)

externalVector (15)

extraChIPs (124)

F

factDesign (146)

fastLiquidAssociation (125)

FastqCleaner (130)

FilterFFPE (111)

FindMyFriends (34)

FISHalyseR (117)

flowBeads (130)

flowcatchR (143)

flowClean (250)

flowClust (699)

flowCore (2435)

flowCyBar (112)

flowDensity (275)

flowFlowJo (25)

flowMatch (135)

flowMeans (165)

flowMerge (157)

flowPeaks (196)

flowPloidy (114)

flowPlots (120)

FlowRepositoryR (32)

flowSpecs (126)

flowStats (457)

flowTrans (157)

flowWorkspace (1066)

fobitools (109)

frenchFISH (87)

FRGEpistasis (112)

frmaTools (140)

funtooNorm (113)

G

G4SNVHunter (37)

GA4GHclient (111)

GA4GHshiny (106)

GAprediction (102)

GateFinder (107)

GBScleanR (128)

gCrisprTools (120)

GCSConnection (10)

GCSFilesystem (9)

GDCRNATools (229)

gene2pathway (15)

GeneAccord (24)

GeneAnswers (58)

geneAttribution (122)

GeneBreak (122)

geneClassifiers (113)

GeneExpressionSignature (160)

genefilter (11540)

GeneGeneInteR (111)

GeneGroupAnalysis (10)

GeneNetworkBuilder (146)

GeneOverlap (636)

geneplast (146)

geneplotter (4398)

geneRecommender (142)

GeneRegionScan (155)

geneRxCluster (137)

GeneSelectMMD (141)

GeneSelector (43)

GeneSpring (13)

GeneStructureTools (121)

geNetClassifier (156)

GeneticsBase (12)

GeneticsDesign (44)

GeneticsPed (158)

GeneTonic (302)

GeneTraffic (12)

geneXtendeR (114)

genomation (656)

GenomAutomorphism (93)

GenomeGraphs (58)

GenomeInfoDb (55129)

genomeIntervals (187)

GenomicAlignments (22633)

GenomicDataCommons (974)

GenomicDistributions (152)

GenomicFeatures (17545)

GenomicFiles (1068)

genomicInstability (116)

GenomicInteractionNodes (96)

GenomicInteractions (399)

GenomicOZone (117)

GenomicPlot (108)

GenomicRanges (45414)

GenomicScores (600)

GenomicSuperSignature (117)

GenomicTuples (128)

Genominator (48)

genotypeeval (38)

GEOexplorer (113)

GEOmetadb (278)

GeomxTools (380)

GEOquery (9882)

GEOsubmission (139)

GeoTcgaData (210)

gff3Plotter (3)

ggseqalign (60)

ggtreeDendro (102)

ggtreeExtra (1159)

ggtreeSpace (82)

GladiaTOX (104)

glmGamPoi (4958)

glmSparseNet (233)

GlobalAncova (994)

globalSeq (111)

globaltest (1765)

GOexpress (154)

GOFunction (43)

GoogleGenomics (22)

goProfiles (161)

GOSemSim (19378)

goSorensen (99)

GOsummaries (56)

granulator (159)

GraphAlignment (123)

graphite (3174)

GreyListChIP (984)

GRmetrics (149)

GSALightning (100)

GSEABase (8736)

GSEABenchmarkeR (130)

GSEAmining (110)

GWAS.BAYES (109)

GWASTools (647)

gwasurvivr (139)

H

HarmonizR (103)

Harshlight (142)

HCAExplorer (6)

HCAMatrixBrowser (2)

HDF5Array (14682)

HelloRanges (133)

hiAnnotator (136)

HiCBricks (164)

HiCcompare (243)

HiCDCPlus (134)

HiCExperiment (171)

HiContacts (162)

hicVennDiagram (91)

HilbertCurve (153)

HilbertVis (205)

HilbertVisGUI (97)

hiReadsProcessor (134)

hmdbQuery (128)

hoodscanR (124)

HPAanalyze (196)

HTSanalyzeR (47)

HTSeqGenie (51)

htSeqTools (44)

HTSFilter (227)

HumanTranscriptomeCompendium (51)

hummingbird (94)

HybridExpress (95)

HybridMTest (164)

hyperdraw (151)

hypergraph (176)

I

iClusterPlus (428)

IdMappingAnalysis (42)

IdMappingRetrieval (40)

IgGeneUsage (104)

illuminaio (2689)

imcRtools (258)

ImmuneSpaceR (36)

immunoClust (128)

immunogenViewer (57)

immunotation (106)

ImpulseDE2 (20)

infercnv (1188)

infinityFlow (122)

Informeasure (97)

inSilicoDb (30)

inSilicoMerging (32)

interacCircos (103)

InteractionSet (1737)

InteractiveComplexHeatmap (423)

interactiveDisplay (154)

interactiveDisplayBase (4163)

InterCellar (117)

InterMineR (89)

IntramiRExploreR (110)

IRanges (55450)

IrisSpatialFeatures (5)

ISAnalytics (85)

iSEEpathways (93)

IsoCorrectoR (137)

IsoCorrectoRGUI (105)

IsoformSwitchAnalyzeR (299)

IsoGeneGUI (54)

iterativeBMA (142)

iterativeBMAsurv (124)

iteremoval (18)

J

JunctionSeq (21)

K

karyoploteR (771)

katdetectr (103)

KEGGgraph (5263)

KEGGlincs (120)

keggorthology (247)

KEGGprofile (48)

KEGGREST (36631)

KinSwingR (108)

knowYourCG (82)

L

LineagePulse (29)

lineagespot (90)

LiquidAssociation (135)

lisaClust (171)

loci2path (117)

LoomExperiment (626)

lpsymphony (856)

LRBaseDbi (115)

LymphoSeq (128)

M

maCorrPlot (130)

MACSQuantifyR (90)

maftools (2523)

MAGeCKFlute (325)

maigesPack (78)

makecdfenv (218)

makePlatformDesign (10)

MantelCorr (120)

maPredictDSC (123)

MassArray (120)

MassSpecWavelet (1697)

matchprobes (13)

MatrixGenerics (42243)

MatrixQCvis (196)

MatrixRider (114)

MaxContrastProjection (15)

MBAmethyl (104)

MCbiclust (120)

MCRestimate (50)

MeasurementError.cor (127)

megadepth (178)

Mergeomics (126)

metabCombiner (156)

MetaboAnnotation (279)

MetaboCoreUtils (1746)

MetaboDynamics (23)

metabolomicsWorkbenchR (124)

metabomxtr (120)

MetaboSignal (156)

metagene2 (127)

metagenomeFeatures (31)

metagenomeSeq (1552)

MetaNeighbor (149)

metaseqR2 (121)

MetaVolcanoR (50)

methimpute (115)

methInheritSim (116)

methodical (67)

MethTargetedNGS (122)

methVisual (42)

methyAnalysis (48)

MethylAid (147)

methylclock (200)

methylGSA (166)

methyLImp2 (92)

methylInheritance (115)

methylKit (671)

MethylMix (161)

methylMnM (132)

methylPipe (142)

methylscaper (133)

MethylSeekR (205)

methylSig (119)

methylumi (1474)

microbiome (1833)

microbiomeDASim (98)

microbiomeExplorer (118)

microbiomeMarker (387)

MicrobiomeProfiler (160)

MicrobiotaProcess (498)

microSTASIS (95)

MinimumDistance (154)

miRBaseConverter (176)

mirIntegrator (126)

miRNAmeConverter (121)

miRNApath (128)

miRspongeR (99)

Mirsynergy (32)

mirTarRnaSeq (110)

missMethyl (1099)

mitoClone2 (114)

mixOmics (2837)

MLInterfaces (403)

MmPalateMiRNA (43)

MobilityTransformR (59)

Modstrings (126)

MoleculeExperiment (113)

Moonlight2R (86)

MoonlightR (131)

Motif2Site (100)

motifbreakR (196)

motifcounter (110)

motifmatchr (1282)

MotifPeeker (28)

motifStack (636)

motifTestR (101)

MPRAnalyze (121)

MsBackendMassbank (111)

MsBackendMetaboLights (55)

MsBackendMgf (473)

MsBackendMsp (383)

MsBackendRawFileReader (102)

MsBackendSql (107)

MsCoreUtils (3468)

MsDataHub (127)

MsExperiment (1315)

MsFeatures (1357)

msmsTests (271)

MSstatsBig (87)

MSstatsBioNet (19)

MSstatsConvert (433)

MSstatsLiP (117)

MSstatsLOBD (99)

MSstatsPTM (202)

MSstatsQC (119)

MSstatsQCgui (100)

MSstatsSampleSize (25)

MSstatsShiny (135)

MSstatsTMT (269)

MSstatsTMTPTM (5)

MultiAssayExperiment (6222)

multiClust (131)

multicrispr (102)

MultiDataSet (1157)

multiGSEA (174)

multiHiCcompare (158)

MultimodalExperiment (87)

multiOmicsViz (45)

MultiRNAflow (105)

multiscan (135)

multiSight (15)

multistateQTL (77)

multiWGCNA (131)

multtest (11783)

MungeSumstats (875)

MutationalPatterns (308)

MWASTools (160)

myvariant (137)

N

NADfinder (114)

NanoMethViz (133)

NanoStringDiff (148)

NanoStringNCTools (374)

NanoStringQCPro (47)

NarrowPeaks (39)

ncdfFlow (1026)

ncRNAtools (105)

nearBynding (98)

Nebulosa (1230)

NeighborNet (33)

NetActivity (93)

netbenchmark (26)

NetPathMiner (120)

netresponse (145)

netSmooth (124)

networkBMA (50)

ngsReports (128)

nipalsMCIA (100)

nondetects (62)

normalize450K (110)

NormalyzerDE (216)

nucleoSim (115)

nullranges (197)

NxtIRFcore (14)

O

oligoClasses (1597)

OmicCircos (238)

omicplotR (114)

omicRexposome (119)

OmicsLonDA (26)

OmicsMarkeR (27)

OmicsMLRepoR (44)

omicsPrint (122)

omicsViewer (100)

OmnipathR (783)

oncoscanR (104)

OncoScore (116)

OncoSimulR (132)

oneChannelGUI (54)

openPrimeR (174)

openPrimeRui (56)

optimalFlow (106)

OrderedList (149)

ORFhunteR (102)

Organism.dplyr (392)

OrganismDbi (2575)

orthogene (369)

P

packFinder (114)

PAIRADISE (144)

paircompviz (124)

pairedGSEA (77)

panelcn.mops (116)

PAnnBuilder (45)

PanVizGenerator (25)

pathifier (140)

pathlinkR (116)

PathoStat (190)

pathRender (143)

pathview (4566)

pathwayPCA (126)

PathwaySplice (14)

PatientGeneSets (6)

paxtoolsr (108)

pcaExplorer (366)

pcaGoPromoter (34)

pcaMethods (5028)

PCAtools (1217)

pdInfoBuilder (181)

peakPantheR (104)

Pedixplorer (81)

PepSetTest (56)

pepXMLTab (125)

periodicDNA (102)

perturbatr (15)

pfamAnalyzeR (267)

phantasus (222)

phantasusLite (102)

PharmacoGx (244)

PhenoGeneRanker (81)

phenopath (138)

phenoTest (156)

phosphonormalizer (96)

PhyloProfile (115)

phyloseq (5501)

Pigengene (135)

pipeFrame (143)

pkgDepTools (68)

planttfhunter (113)

plotgardener (230)

plotGrouper (98)

PLSDAbatch (103)

plyinteractions (97)

plyranges (1073)

polyester (122)

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