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

Download stats for Bioconductor software packages

Data as of Mon. 01 Dec 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 (66110)	26	edgeR (25644)	51	assorthead (13523)
2	BiocGenerics (63980)	27	treeio (25314)	52	BiocSingular (13399)
3	IRanges (59455)	28	Rhtslib (24875)	53	ScaledMatrix (13148)
4	S4Vectors (59097)	29	Rhdf5lib (24787)	54	BSgenome (12723)
5	GenomeInfoDb (58910)	30	rhdf5 (23987)	55	genefilter (12592)
6	BiocParallel (55515)	31	GenomicAlignments (23709)	56	AnnotationHub (12063)
7	XVector (54887)	32	enrichplot (23253)	57	multtest (11959)
8	Biobase (54633)	33	rhdf5filters (23059)	58	ProtGenerics (11824)
9	Biostrings (50667)	34	clusterProfiler (23053)	59	BiocNeighbors (11758)
10	SparseArray (48380)	35	DOSE (22903)	60	AnnotationFilter (11526)
11	GenomicRanges (48156)	36	biomaRt (22174)	61	impute (11490)
12	DelayedArray (46201)	37	qvalue (21740)	62	GEOquery (11122)
13	MatrixGenerics (46130)	38	graph (21261)	63	GSEABase (9797)
14	SummarizedExperiment (45291)	39	rtracklayer (21232)	64	ensembldb (9770)
15	S4Arrays (44589)	40	GOSemSim (21159)	65	scuttle (9636)
16	UCSC.utils (42872)	41	BiocIO (20156)	66	Rgraphviz (9537)
17	AnnotationDbi (39897)	42	SingleCellExperiment (18398)	67	RBGL (9239)
18	KEGGREST (39859)	43	ComplexHeatmap (18359)	68	VariantAnnotation (8955)
19	limma (37778)	44	annotate (18339)	69	affyio (8692)
20	zlibbioc (36622)	45	GenomicFeatures (17884)	70	ExperimentHub (8572)
21	BiocFileCache (27363)	46	beachmat (16792)	71	affy (8482)
22	Rsamtools (26197)	47	DelayedMatrixStats (16665)	72	sva (8304)
23	DESeq2 (26145)	48	sparseMatrixStats (16249)	73	GSVA (8056)
24	ggtree (26036)	49	preprocessCore (15495)	74	BiocBaseUtils (8018)
25	fgsea (25850)	50	HDF5Array (15344)	75	pwalign (7822)

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 (198)

a4Preproc (242)

a4Reporting (192)

ABAEnrichment (59)

adductomicsR (164)

adverSCarial (126)

affxparser (1916)

AffyCompatible (82)

affyContam (196)

affycoretools (478)

AffyExpress (53)

affylmGUI (231)

affyQCReport (55)

AffyRNADegradation (189)

AffyTiling (32)

aggregateBioVar (184)

Agi4x44PreProcess (28)

AgiMicroRna (287)

AHMassBank (128)

alabaster (136)

alabaster.base (4304)

alabaster.bumpy (137)

alabaster.files (126)

alabaster.mae (144)

alabaster.matrix (4045)

alabaster.ranges (3960)

alabaster.sce (1275)

alabaster.schemas (3890)

alabaster.se (3924)

alabaster.sfe (68)

alabaster.spatial (142)

alabaster.string (135)

alabaster.vcf (133)

AllelicImbalance (215)

AlphaBeta (182)

AlphaMissenseR (145)

altcdfenvs (208)

AMOUNTAIN (201)

ampliQueso (40)

AnalysisPageServer (39)

AneuFinder (186)

anglemania (15)

animalcules (231)

AnnBuilder (11)

annotate (18339)

AnnotationDbi (39897)

AnnotationFilter (11526)

AnnotationForge (1934)

AnnotationFuncs (41)

AnnotationHub (12063)

AnnotationHubData (407)

annotationTools (227)

anota2seq (241)

antiProfiles (173)

AnVILBase (481)

AnVILBilling (149)

AnVILPublish (141)

AnVILWorkflow (131)

apComplex (198)

appreci8R (175)

aroma.light (1805)

ArrayExpress (490)

ArrayExpressHTS (43)

arrayMagic (17)

arrayMvout (183)

arrayQCplot (7)

arrayQuality (322)

arrayQualityMetrics (592)

ArrayTools (52)

ARRmNormalization (179)

AssessORF (183)

assorthead (13523)

ATACCoGAPS (20)

ATACseqQC (526)

ATACseqTFEA (155)

autonomics (172)

AWAggregator (23)

B

BadRegionFinder (160)

ballgown (1190)

bamsignals (1101)

barcodetrackR (160)

basecallQC (189)

BaseSpaceR (178)

Basic4Cseq (187)

BASiCStan (142)

BasicSTARRseq (162)

basilisk (3677)

basilisk.utils (3402)

batchelor (4215)

BayesKnockdown (161)

BayesSpace (459)

BBCAnalyzer (196)

BDMMAcorrect (41)

beachmat (16792)

beachmat.hdf5 (242)

beachmat.tiledb (94)

beadarray (697)

beadarraySNP (83)

BeadDataPackR (670)

BeadExplorer (8)

benchdamic (118)

bigmemoryExtras (36)

BindingSiteFinder (166)

bioassayR (192)

Biobase (54633)

biobtreeR (133)

bioCancer (182)

BioCartaImage (129)

BiocBaseUtils (8018)

BiocCaseStudies (56)

BiocCheck (1664)

biocDatasets (6)

BiocDockerManager (25)

BiocFileCache (27363)

BiocGenerics (63980)

biocGraph (234)

BiocHubsShiny (163)

BiocInstaller (125)

BiocNeighbors (11758)

BiocOncoTK (70)

BiocParallel (55515)

BiocPkgTools (301)

biocroxytest (117)

BiocSingular (13399)

BiocSklearn (219)

BiocStyle (6217)

BiocVersion (66110)

biocViews (4422)

BiocWorkflowTools (239)

biodbChebi (158)

biodbExpasy (22)

biodbHmdb (138)

biodbLipidmaps (25)

biodbMirbase (18)

biodbNcbi (140)

biodbUniprot (126)

biomaRt (22174)

biomformat (6200)

BioMVCClass (194)

biomvRCNS (193)

BioNetStat (54)

BioSeqClass (61)

biosigner (185)

Biostrings (50667)

biovizBase (5521)

biscuiteer (173)

blacksheepr (180)

BloodGen3Module (170)

brainflowprobes (44)

brainImageR (10)

BrainSABER (27)

BrainStars (41)

branchpointer (184)

breakpointR (181)

BreastSubtypeR (101)

BRGenomics (80)

BridgeDbR (218)

BrowserViz (236)

BrowserVizDemo (12)

BSgenome (12723)

BSgenomeForge (265)

BubbleTree (191)

BufferedMatrix (178)

BufferedMatrixMethods (181)

bugsigdbr (588)

BulkSignalR (141)

bumphunter (2498)

BumpyMatrix (575)

BUScorrect (177)

C

CAGEfightR (276)

cageminer (167)

CalibraCurve (13)

cancerclass (460)

CancerInSilico (54)

CancerMutationAnalysis (61)

CancerSubtypes (111)

cardelino (161)

CardinalIO (257)

Category (1318)

categoryCompare (216)

CatsCradle (123)

cBioPortalData (516)

cbpManager (162)

CCPROMISE (175)

CellaRepertorium (45)

CellBarcode (174)

cellbaseR (180)

CellBench (243)

cellGrowth (34)

CellMapper (158)

cellmigRation (152)

CellNOptR (281)

cellscape (149)

CellScore (127)

CellTrails (196)

cellxgenedp (171)

ceRNAnetsim (148)

CGHnormaliter (198)

CGHregions (184)

ChemmineOB (400)

ChemmineR (925)

chevreulPlot (98)

chevreulProcess (105)

chevreulShiny (76)

chimeraviz (215)

ChIPanalyser (209)

chipenrich (243)

ChIPexoQual (184)

ChIPpeakAnno (1018)

ChIPseeker (2391)

ChIPSeqSpike (29)

ChIPXpress (164)

chopsticks (206)

Chromatograms (18)

chromDraw (183)

ChromHeatMap (206)

chromPlot (220)

ChromSCape (159)

chromstaR (102)

chromswitch (55)

chromVAR (1294)

cigarillo (1293)

circRNAprofiler (191)

CircSeqAlignTk (131)

ClassifyR (382)

cleanUpdTSeq (224)

CleanUpRNAseq (124)

cliProfiler (146)

clonotypeR (44)

clstutils (194)

clustComp (165)

clusterExperiment (433)

ClusterFoldSimilarity (131)

ClusterGVis (1)

ClusterJudge (172)

clusterProfiler (23053)

clusterSeq (169)

ClusterSignificance (182)

clusterStab (196)

clustifyr (273)

clustSIGNAL (99)

CNORfeeder (182)

CNORfuzzy (187)

CNVfilteR (139)

CNVMetrics (153)

CNVPanelizer (181)

CNVRanger (203)

CoCiteStats (181)

coMethDMR (158)

compartmap (54)

compcodeR (246)

compEpiTools (172)

ComplexHeatmap (18359)

CompoundDb (374)

concordexR (140)

condiments (216)

consensus (164)

ConsensusClusterPlus (2991)

consensusDE (165)

consensusOV (185)

consensusSeekeR (185)

COPDSexualDimorphism (7)

copynumber (178)

CopyNumber450k (20)

CopyNumberPlots (180)

CopywriteR (57)

CountClust (46)

countsimQC (205)

CoverageView (193)

CRISPRball (109)

crisprBase (215)

crisprBowtie (187)

crisprBwa (125)

crisprDesign (208)

crisprScore (220)

CRISPRseek (278)

crisprseekplus (36)

crisprShiny (117)

CrispRVariants (240)

crisprVerse (154)

crisprViz (169)

crossmeta (100)

CTDquerier (173)

CTexploreR (124)

cummeRbund (370)

CuratedAtlasQueryR (148)

customCMPdb (138)

customProDB (181)

cyanoFilter (154)

CyTOFpower (79)

cytoKernel (152)

cytomapper (456)

CytoPipeline (153)

CytoPipelineGUI (123)

cytoviewer (171)

D

DAMEfinder (181)

dandelionR (106)

DAVIDQuery (28)

ddPCRclust (193)

debrowser (233)

DECIPHER (3118)

DEComplexDisease (51)

decompTumor2Sig (185)

DeconRNASeq (383)

decontam (1725)

DeconvoBuddies (97)

decoupleR (1732)

DeeDeeExperiment (25)

DeepPINCS (155)

DeepTarget (120)

DEFormats (333)

DEGreport (675)

DelayedArray (46201)

DelayedDataFrame (154)

DelayedMatrixStats (16665)

DelayedRandomArray (154)

DelayedTensor (152)

deltaCaptureC (143)

deltaGseg (182)

derfinder (609)

derfinderHelper (591)

derfinderPlot (230)

DiffBind (1261)

diffcoexp (202)

DifferentialRegulation (154)

diffGeneAnalysis (177)

diffuStats (195)

dir.expiry (4223)

DirichletMultinomial (4516)

discordant (207)

DiscoRhythm (185)

dittoSeq (1392)

divergence (159)

DMRcaller (227)

DMRforPairs (71)

DNABarcodeCompatibility (136)

DNABarcodes (261)

DNAfusion (151)

DNAshapeR (251)

domainsignatures (35)

DominoEffect (149)

dominoSignal (122)

doppelgangR (172)

doubletrouble (166)

drawProteins (272)

DriverNet (200)

DropletUtils (2554)

drugTargetInteractions (155)

DrugVsDisease (180)

DupChecker (23)

DuplexDiscovereR (119)

E

EasyCellType (167)

easyreporting (163)

easyRNASeq (236)

EBcoexpress (194)

EDIRquery (137)

EmpiricalBrownsMethod (201)

ENCODExplorer (45)

EnhancedVolcano (6589)

enhancerHomologSearch (149)

EnrichedHeatmap (870)

EnrichmentBrowser (535)

enrichplot (23253)

enrichViewNet (136)

ensembldb (9770)

ensemblVEP (108)

ENVISIONQuery (39)

epialleleR (171)

EpiCompare (159)

epidecodeR (151)

epigenomix (174)

epigraHMM (194)

epimutacions (155)

epiregulon (123)

epiregulon.extra (132)

epistasisGA (140)

epivizrChart (177)

epivizrData (180)

epivizrServer (183)

epivizrStandalone (175)

erccdashboard (207)

eudysbiome (192)

evaluomeR (157)

EventPointer (199)

ExCluster (147)

exomeCopy (215)

exomePeak2 (103)

ExperimentHub (8572)

ExperimentHubData (347)

ExperimentSubset (155)

ExploreModelMatrix (353)

ExpressionAtlas (213)

ExpressionView (64)

exprExternal (2)

externalVector (14)

extraChIPs (172)

F

factDesign (188)

fastLiquidAssociation (164)

FastqCleaner (205)

FeatSeekR (123)

FilterFFPE (158)

FindMyFriends (44)

FISHalyseR (155)

flowBeads (182)

flowcatchR (209)

flowClean (308)

flowClust (877)

flowCore (2685)

flowCyBar (151)

flowDensity (393)

flowFlowJo (34)

flowGraph (157)

flowMatch (189)

flowMeans (271)

flowMerge (208)

flowPeaks (286)

flowPloidy (172)

flowPlots (163)

FlowRepositoryR (31)

flowSpecs (177)

flowStats (624)

flowTrans (210)

flowWorkspace (1312)

fobitools (158)

frenchFISH (127)

FRGEpistasis (152)

frmaTools (199)

funtooNorm (169)

G

G4SNVHunter (133)

GA4GHclient (158)

GA4GHshiny (149)

GAprediction (146)

GateFinder (146)

GBScleanR (150)

gCrisprTools (214)

GCSConnection (16)

GCSFilesystem (12)

GDCRNATools (301)

gDRimport (133)

gene2pathway (15)

GeneAccord (43)

GeneAnswers (95)

geneAttribution (195)

GeneBreak (186)

geneClassifiers (179)

GeneExpressionSignature (220)

genefilter (12592)

GeneGeneInteR (118)

GeneGroupAnalysis (11)

GeneNetworkBuilder (228)

GeneOverlap (898)

geneplast (207)

geneplotter (3977)

geneRecommender (187)

GeneRegionScan (217)

geneRxCluster (181)

GeneSelectMMD (189)

GeneSelector (43)

GeneSpring (15)

GeneStructureTools (191)

geNetClassifier (223)

GeneticsBase (16)

GeneticsDesign (41)

GeneticsPed (220)

GeneTonic (272)

GeneTraffic (12)

geneXtendeR (185)

genomation (824)

GenomAutomorphism (154)

GenomeGraphs (63)

GenomeInfoDb (58910)

genomeIntervals (255)

GenomicAlignments (23709)

GenomicDataCommons (1004)

GenomicDistributions (214)

GenomicFeatures (17884)

GenomicFiles (1045)

genomicInstability (168)

GenomicInteractionNodes (142)

GenomicInteractions (441)

GenomicOZone (151)

GenomicPlot (159)

GenomicRanges (48156)

GenomicScores (686)

GenomicSuperSignature (186)

GenomicTuples (186)

Genominator (58)

genotypeeval (40)

GenProSeq (141)

GEOexplorer (158)

GEOmetadb (384)

geomeTriD (124)

GeomxTools (471)

GEOquery (11122)

GEOsubmission (184)

GeoTcgaData (172)

gff3Plotter (5)

ggseqalign (105)

ggtreeDendro (145)

ggtreeExtra (1579)

ggtreeSpace (117)

ginmappeR (116)

gINTomics (133)

GladiaTOX (165)

glmGamPoi (5938)

glmSparseNet (223)

GlobalAncova (1166)

globalSeq (165)

globaltest (1750)

GOexpress (251)

GOFunction (49)

GoogleGenomics (20)

goProfiles (234)

GOSemSim (21159)

goSorensen (142)

GOsummaries (101)

granulator (201)

GraphAlignment (173)

graphite (4065)

GreyListChIP (1154)

GRmetrics (210)

GSALightning (154)

GSEABase (9797)

GSEABenchmarkeR (191)

GSEAmining (183)

GWAS.BAYES (156)

GWASTools (740)

gwasurvivr (174)

H

HarmonizR (169)

Harshlight (139)

HCABrowser (10)

HCAExplorer (7)

HCAMatrixBrowser (4)

HDF5Array (15344)

HelloRanges (249)

hiAnnotator (205)

HiCBricks (238)

HiCcompare (393)

HiCDCPlus (180)

HiCExperiment (216)

HiContacts (210)

hicVennDiagram (143)

HilbertCurve (218)

HilbertVis (244)

HilbertVisGUI (115)

hiReadsProcessor (179)

hmdbQuery (171)

HoloFoodR (118)

hoodscanR (184)

HPAanalyze (281)

HTSanalyzeR (57)

HTSeqGenie (32)

htSeqTools (59)

HTSFilter (311)

HumanTranscriptomeCompendium (58)

hummingbird (139)

HybridExpress (129)

HybridMTest (215)

hyperdraw (200)

hypergraph (232)

I

iClusterPlus (464)

IdMappingAnalysis (57)

IdMappingRetrieval (35)

IgGeneUsage (168)

illuminaio (2771)

imcRtools (327)

immReferent (0)

ImmuneSpaceR (85)

immunoClust (180)

immunogenViewer (92)

immunotation (176)

ImpulseDE2 (21)

iNETgrate (125)

infercnv (1561)

infinityFlow (156)

Informeasure (136)

inSilicoDb (27)

inSilicoMerging (28)

interacCircos (139)

InteractionSet (1679)

InteractiveComplexHeatmap (543)

interactiveDisplay (256)

interactiveDisplayBase (3154)

InterCellar (178)

InterMineR (87)

IntramiRExploreR (171)

IRanges (59455)

IrisSpatialFeatures (8)

ISAnalytics (164)

iSEEindex (136)

iSEEpathways (138)

IsoCorrectoR (203)

IsoCorrectoRGUI (136)

IsoformSwitchAnalyzeR (437)

IsoGeneGUI (76)

iterativeBMA (190)

iterativeBMAsurv (168)

iteremoval (23)

J

JunctionSeq (31)

K

karyoploteR (968)

katdetectr (140)

KEGGgraph (5922)

KEGGlincs (180)

keggorthology (205)

KEGGprofile (52)

KEGGREST (39859)

KinSwingR (160)

knowYourCG (138)

L

Lheuristic (78)

LineagePulse (42)

lineagespot (138)

LipidTrend (46)

LiquidAssociation (175)

lisaClust (252)

loci2path (145)

looking4clusters (14)

LoomExperiment (660)

lpsymphony (1087)

LRBaseDbi (148)

LymphoSeq (184)

M

Maaslin2 (1073)

maCorrPlot (192)

MACSQuantifyR (143)

maftools (2713)

MAGeCKFlute (273)

maigesPack (102)

makecdfenv (317)

makePlatformDesign (11)

MantelCorr (167)

maPredictDSC (168)

MassArray (170)

MassSpecWavelet (1942)

matchprobes (18)

MatrixGenerics (46130)

MatrixQCvis (173)

MatrixRider (170)

MaxContrastProjection (23)

MBAmethyl (150)

MCbiclust (195)

MCRestimate (47)

MeasurementError.cor (170)

megadepth (222)

Mergeomics (194)

metabCombiner (216)

MetaboAnnotation (261)

MetaboCoreUtils (2528)

MetaboDynamics (113)

metabolomicsWorkbenchR (192)

metabomxtr (164)

MetaboSignal (222)

metagene2 (186)

metagenomeFeatures (40)

metagenomeSeq (1857)

MetaNeighbor (255)

metaseqR2 (187)

MetaVolcanoR (78)

methimpute (185)

methInheritSim (161)

methodical (109)

MethTargetedNGS (161)

methVisual (43)

methyAnalysis (63)

MethylAid (214)

methylclock (302)

methylGSA (223)

methyLImp2 (136)

methylInheritance (184)

methylKit (904)

MethylMix (229)

methylMnM (205)

methylPipe (186)

methylscaper (160)

MethylSeekR (322)

methylSig (208)

methylumi (1463)

microbiome (2171)

microbiomeDASim (152)

microbiomeExplorer (165)

microbiomeMarker (400)

MicrobiomeProfiler (195)

MicrobiotaProcess (562)

microSTASIS (127)

MinimumDistance (199)

miRBaseConverter (326)

mirIntegrator (188)

miRNAmeConverter (168)

miRNApath (170)

miRspongeR (162)

Mirsynergy (33)

mirTarRnaSeq (164)

missMethyl (1176)

mitoClone2 (157)

mixOmics (3511)

MLInterfaces (486)

MmPalateMiRNA (53)

mobileRNA (125)

MobilityTransformR (15)

Modstrings (200)

MoleculeExperiment (150)

Moonlight2R (142)

MoonlightR (198)

Motif2Site (151)

motifbreakR (332)

motifcounter (160)

motifmatchr (1468)

MotifPeeker (111)

motifStack (813)

motifTestR (140)

MPRAnalyze (179)

MsBackendMassbank (171)

MsBackendMetaboLights (140)

MsBackendMgf (568)

MsBackendMsp (370)

MsBackendRawFileReader (177)

MsBackendSql (139)

MsCoreUtils (3791)

MsDataHub (194)

MsExperiment (1474)

MsFeatures (1585)

msmsTests (348)

MsQuality (151)

MSstatsBig (132)

MSstatsBioNet (99)

MSstatsConvert (614)

MSstatsLiP (168)

MSstatsLOBD (134)

MSstatsPTM (304)

MSstatsQC (180)

MSstatsQCgui (140)

MSstatsResponse (11)

MSstatsSampleSize (44)

MSstatsShiny (184)

MSstatsTMT (387)

MSstatsTMTPTM (7)

MultiAssayExperiment (6636)

multiClust (204)

multicrispr (165)

MultiDataSet (1442)

multiGSEA (212)

multiHiCcompare (239)

MultimodalExperiment (138)

multiOmicsViz (67)

MultiRNAflow (142)

multiscan (181)

multiSight (27)

multistateQTL (119)

multiWGCNA (167)

multtest (11959)

MungeSumstats (773)

MutationalPatterns (461)

MWASTools (215)

myvariant (216)

N

NADfinder (173)

NanoMethViz (196)

NanoStringDiff (197)

NanoStringNCTools (465)

NanoStringQCPro (65)

NarrowPeaks (39)

ncdfFlow (1227)

ncRNAtools (144)

nearBynding (170)

Nebulosa (1299)

NeighborNet (44)

NetActivity (128)

netbenchmark (26)

NetPathMiner (206)

netresponse (196)

netSmooth (183)

networkBMA (71)

ngsReports (207)

nipalsMCIA (148)

nondetects (137)

normalize450K (166)

NormalyzerDE (314)

notameStats (14)

nucleoSim (167)

nullranges (284)

NxtIRFcore (40)

O

oligoClasses (1862)

OmicCircos (310)

omicplotR (170)

omicRexposome (182)

OmicsLonDA (44)

OmicsMarkeR (22)

OmicsMLRepoR (96)

omicsPrint (180)

omicsViewer (165)

OmnipathR (1069)

oncoscanR (154)

OncoScore (154)

OncoSimulR (216)

oneChannelGUI (64)

onlineFDR (136)

openPrimeR (203)

openPrimeRui (59)

OpenStats (131)

optimalFlow (154)

OrderedList (209)

ORFhunteR (163)

Organism.dplyr (398)

OrganismDbi (2918)

orthogene (611)

OSTA.data (127)

OutSplice (143)

P

packFinder (173)

PAIRADISE (193)

paircompviz (175)

pairedGSEA (118)

panelcn.mops (192)

PAnnBuilder (42)

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Y

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