SummarizedExperiment

Depends On Me (177): AffiXcan, airway, alabaster.se, AllelicImbalance, atena, bambu, batchCorr, betaHMM, betterChromVAR, BiocSklearn, BioPlex, BiSeq, bnbc, bodymapRat, broadSeq, bsseq, CAGEfightR, celaref, celldex, clusterExperiment, CoreGx, coseq, csaw, CSSQ, curatedAdipoChIP, curatedAdipoRNA, curatedMetagenomicData, DaMiRseq, deepSNV, DeMixT, DESeq2, DEXSeq, DiffBind, diffcoexp, diffHic, dinoR, divergence, DMCFB, DMCHMM, dmGsea, DRomics, ENmix, EnrichmentBrowser, epigenomix, evaluomeR, EventPointer, ExperimentSubset, ExpressionAtlas, extraChIPs, FEAST, fission, FRASER, GenomicAlignments, GenomicFiles, GenomicSuperSignature, GRmetrics, GSEABenchmarkeR, GSVAdata, HDCytoData, HelloRanges, hermes, HERON, HiCDOC, HighlyReplicatedRNASeq, hipathia, HMP16SData, HumanRetinaLRSData, InTAD, InteractionSet, IntEREst, iSEE, iSEEhex, iSEEhub, iSEEindex, ISLET, isomiRs, ivygapSE, lefser, LimROTS, lipidr, LoomExperiment, Macarron, made4, MatrixQCvis, MBASED, MetaGxOvarian, MetaGxPancreas, methodical, methrix, methylPipe, MethylSeqData, MetNet, MGnifyR, mia, miaViz, MicrobiomeBenchmarkData, microbiomeDataSets, microRNAome, MICSQTL, minfi, moanin, MouseGastrulationData, MouseThymusAgeing, mpra, MultiAssayExperiment, multistateQTL, NADfinder, NBAMSeq, NewWave, notame, notameStats, notameViz, ObMiTi, OncoSubtype, ordinalbayes, orthos, OUTRIDER, padma, PDATK, phenomis, PhIPData, PlinkMatrix, profileplyr, PRONE, qmtools, qsvaR, QTLExperiment, recount, recount3, ReducedExperiment, RegEnrich, REMP, RFLOMICS, ROCpAI, rqt, sampleClassifierData, Scale4C, scAnnotatR, scGPS, scMultiome, scone, screenCounter, scTreeViz, SDAMS, sechm, SeqGate, SEtools, SGSeq, signatureSearch, SingleCellExperiment, singleCellTK, SingleR, soGGi, spatialDmelxsim, spillR, spqn, spqnData, sRACIPE, ssPATHS, stageR, survtype, TENxIO, tidyCoverage, tidySummarizedExperiment, timecoursedata, TissueEnrich, TREG, tuberculosis, TumourMethData, UMI4Cats, VanillaICE, VariantAnnotation, VariantExperiment, velociraptor, weitrix, yamss, zinbwave

Imports Me (584): ADAM, ADImpute, aggregateBioVar, airpart, alabaster.sfe, ALDEx2, anansi, anglemania, animalcules, anota2seq, APAlyzer, apeglm, APL, appreci8R, ASICS, ASURAT, asuri, atacInferCnv, ATACseqTFEA, AUCell, autoGO, autonomics, awst, Banksy, barbieQ, barcodetrackR, BASiCS, BASiCStan, BatChef, batchelor, BatchQC, BatchSVG, Battlefield, BayesSpace, bayNorm, BBCAnalyzer, beer, benchdamic, BERT, bettr, BioGA, bioLeak, BioNERO, biosigner, biotmle, biovizBase, biscuiteer, BiSeq, blacksheepr, blase, blisa, BloodCancerMultiOmics2017, BloodGen3Module, BreastSubtypeR, brgedata, BulkSignalR, BUMHMM, BUScorrect, BUSseq, CaDrA, CAEN, CAGEr, CalibraCurve, CARDspa, carnation, CATALYST, CatsCradle, cBioPortalData, ccfindR, ccImpute, CDI, celda, CelliD, CellMixS, CellTrails, censcyt, Cepo, CeTF, CHETAH, ChIPpeakAnno, ChromSCape, chromVAR, CiteFuse, CleanUpRNAseq, CLLmethylation, ClusterGVis, clustifyr, clustSIGNAL, cmapR, CNVfilteR, CNVRanger, CoGAPS, comapr, combi, concordexR, condiments, consICA, CopyNumberPlots, Coralysis, corral, COSMIC.67, COTAN, countsimQC, CPSM, CrcBiomeScreen, crupR, CSOA, CTexploreR, CTSV, CuratedAtlasQueryR, curatedTCGAData, cydar, cypress, CyTOFpower, cytofQC, cytoKernel, cytomapper, cytoviewer, DAMEfinder, dandelionR, debrowser, decemedip, decompTumor2Sig, decontX, DeconvoBuddies, DeeDeeExperiment, DEFormats, DEGreport, DELocal, deltaCaptureC, demuxSNP, DenoIST, DEScan2, DESpace, destiny, DEWSeq, diffcyt, DifferentialRegulation, diffUTR, Dino, DiscoRhythm, distinct, dittoSeq, DMRcate, DNEA, dominatR, DominoEffect, doppelgangR, DoReMiTra, doseR, DOTSeq, dreamlet, DropletUtils, DspikeIn, Dune, DWLS, easierData, easyRNASeq, eisaR, ELMER, emtdata, EMTscoreData, epigraHMM, EpiMix, epimutacions, epiregulon, epiregulon.extra, epiSeeker, epistack, epivizrData, escape, escheR, EWCE, ExpHunterSuite, ExpoRiskR, fcScan, FeatSeekR, FieldEffectCrc, findIPs, FindIT2, fishpond, FLAMES, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, fluentGenomics, FuseSOM, G4SNVHunter, GARS, gCrisprTools, gDNAx, gDRcore, gDRimport, gDRutils, gemma.R, GeneTonic, genomicInstability, GEOquery, GeoTcgaData, getDEE2, geyser, ggbio, ggsc, ggspavis, gINTomics, Glimma, glmGamPoi, glmSparseNet, glycoTraitR, GNET2, GRaNIE, GraphExperiment, GreyListChIP, gscreend, GSE13015, GSVA, gwasurvivr, GWENA, HarmonizR, HCATonsilData, HiBED, HiContacts, HiCParser, hicream, HistoImagePlot, HMP2Data, HoloFoodR, hoodscanR, humanHippocampus2024, hummingbird, HybridExpress, iasva, Ibex, icetea, ideal, IFAA, IgGeneUsage, IHWpaper, ILoReg, imageFeatureTCGA, imageTCGAutils, imcExperiment, imcRtools, immLynx, iModMix, iNETgrate, infercnv, INSPEcT, iSEEde, iSEEfier, iSEEpathways, iSEEtree, iSEEu, IsoBayes, IsoformSwitchAnalyzeR, karyotapR, kmcut, LACE, leapR, LegATo, lemur, limpca, lineagespot, lionessR, LipidTrend, lisaClust, looking4clusters, MAI, mariner, marr, MAST, mastR, mbkmeans, MBQN, mCSEA, MEAL, MEAT, MEB, MerfishData, MetaboAnnotation, MetaboDynamics, metabolomicsWorkbenchR, MetaGxBreast, MetAlyzer, MetaNeighbor, MetaProViz, MetaScope, metaseqR2, MethReg, MethylAid, methyLImp2, methylscaper, methylumi, miaDash, miaSim, miaTime, microbial, MicrobiotaProcess, midasHLA, mikropml, miloR, MinimumDistance, miRLAB, miRSM, missMethyl, mist, MLInterfaces, MLSeq, mobileRNA, monaLisa, MoonlightR, mosdef, motifbreakR, motifmatchr, MotifPeeker, MPAC, MPRAnalyze, MsExperiment, MsFeatures, msgbsR, mspms, MSPrep, msqrob2, MuData, MultiDataSet, multimedia, MultiRNAflow, multiWGCNA, mumosa, muscat, musicatk, mutscan, MutSeqR, MWASTools, NanoMethViz, Nebulosa, NetActivity, netSmooth, nipalsMCIA, nnSVG, NoRCE, NormalyzerDE, OAtools, oligoClasses, omicRexposome, omicsGMF, omicsPrint, omicsViewer, omXplore, oncomix, ontoProc, ORFik, orthosData, OVESEG, PAIRADISE, pairedGSEA, pairkat, parati, pcaExplorer, peco, PepSetTest, pgxRpi, PharmacoGx, phenopath, PhosR, pipeComp, Pirat, PIUMA, plaid, planttfhunter, PlasmaMutationDetector, plyxp, pmp, poem, PolySTest, POMA, POWSC, proActiv, proBatch, proDA, psichomics, PureCN, QFeatures, qsmooth, quantiseqr, R453Plus1Toolbox, RadioGx, raer, RaggedExperiment, RankMap, RareVariantVis, RBedMethyl, RcisTarget, RCPA, ReactomeGSA, receptLoss, RegionalST, regionReport, regsplice, RFGeneRank, rgsepd, rifi, rifiComparative, Rmmquant, RNAAgeCalc, RNAsense, RNAseqQC, RnaSeqSampleSize, RNAshapeQC, roar, ROCnGO, RolDE, ropls, rScudo, RTCGAToolbox, RTN, RUCova, SanityR, saseR, satuRn, SBGNview, SC3, scafari, SCArray, SCArray.sat, scater, scBFA, scCB2, scConform, scDblFinder, scDD, scDDboost, scDesign3, scDiagnostics, scds, scECODA, scGraphVerse, scHOT, scider, scLang, scmap, scMerge, scMET, scmeth, scMultiSim, SCnorm, scoreInvHap, scp, scPipe, scQTLtools, scran, scReClassify, scRepertoire, scRNAseq, scROSHI, scruff, scry, scTensor, scTGIF, scuttle, scviR, segmenter, seqCAT, SEraster, sesame, sfi, SGCP, shinyDSP, sigFeature, signifinder, SigsPack, SimBu, simPIC, simpleSeg, singIST, SingleCellAlleleExperiment, SingleCellMultiModal, singscore, slalom, slingshot, smartid, SmartPhos, smoothclust, smoppix, snapcount, SNPhood, sosta, SpaceTrooper, spacexr, Spaniel, SpaNorm, spARI, spaSim, SpatialArtifacts, SpatialCPie, spatialDE, SpatialExperiment, spatialFDA, SpatialFeatureExperiment, spatialHeatmap, spatialLIBD, spatialSimGP, spatzie, SPIAT, spicyR, splatter, SpliceImpactR, SpliceWiz, SplicingFactory, SplineDV, SpNeigh, spoon, SpotClean, SpotSweeper, srnadiff, sSNAPPY, StabMap, standR, StatescopeR, Statial, stJoincount, stPipe, struct, StructuralVariantAnnotation, supersigs, SurfR, SVMDO, SVP, switchde, systemPipeR, systemPipeTools, TabulaMurisSenisData, TBSignatureProfiler, TCGAbiolinks, TCGAutils, TCGAWorkflowData, TCseq, TENET, TENET.ExperimentHub, tenXplore, TENxXeniumData, TFutils, tidybulk, tidyexposomics, tidyprint, tidySingleCellExperiment, tidySpatialExperiment, TOAST, tomoda, ToxicoGx, tpSVG, tradeSeq, TrajectoryUtils, transformGamPoi, transmogR, treeclimbR, treediff, TreeSummarizedExperiment, Trendy, tricycle, TSCAN, TTMap, TVTB, tximeta, UCell, UPDhmm, VAExprs, VariantFiltering, VDJdive, vidger, VisiumIO, visiumStitched, VISTA, vmrseq, Voyager, VSOLassoBag, wpm, XAItest, xCell2, xcms, XeniumIO, xenLite, zellkonverter, zFPKM, zitools

Suggests Me (116): alabaster.mae, AlpsNMR, ANCOMBC, anndataR, AnnotationHub, BindingSiteFinder, biobroom, BiocPkgTools, biomformat, biotmleData, CAEN, cageminer, CAGEWorkflow, Canek, CCAFE, CimpleG, clustree, conos, CTdata, curatedAdipoArray, curatedTBData, CytoSimplex, dar, dcanr, dearseq, decoupleR, DelayedArray, dependentsimr, dorothea, DOtools, DuoClustering2018, dyngen, easier, edgeR, EnMCB, epialleleR, epivizr, epivizrChart, esetVis, file2meco, fobitools, funOmics, gDR, gDRtestData, GENIE3, GenomicRanges, ggmlR, ggpicrust2, globalSeq, GSE103322, gsean, hca, HDF5Array, HPiP, HVP, Informeasure, InteractiveComplexHeatmap, iscream, knowYourCG, lfc, lstar, maaslin3, MatrixGenerics, methFuse, microSTASIS, MiscMetabar, mitology, MOFA2, MSnbase, multiWGCNAdata, parafac4microbiome, pathMED, pathwayPCA, philr, PLSDAbatch, podkat, polyRAD, pRolocdata, PSMatch, R.ComDim, RaceID, radEmu, RforProteomics, RiboProfiling, rliger, Rvisdiff, S4Vectors, SBGNview.data, scFeatureFilter, scLANE, scPassport, scrapper, scToppR, scTypeEval, semisup, seqgendiff, SETA, Seurat, Signac, singleCellHaystack, sketchR, sparrow, speakeasyR, SPOTlight, SuperCell, svaNUMT, svaRetro, SVG, systemPipeShiny, TaxSEA, teal.slice, tidydr, tidytof, tissueTreg, updateObject, volcano3D