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All packages in 'biocstaging' (JSON format)All packages 'biocstaging' (NDJSON stream)BamScaleRbHIVEbppgBreedingExperimentCanvasXpressBiocascadeRCDEnrichcellchatrcellpaintrcircaTimeClinicalVariantRCMEntconsensusRegionsconsensusTADsConvergeRcpgdirectioncpgdirectionDatacrossarrayEWASDEPDgeaHeatmapdmsadrugannotRECLIPSEepiPortraitepiwrapsexposomeSCfaissRfastEmbedRfastPLSgDRplotsGDSAnnotatorGENCODEHubGeneSCARABgeneticumapGeneTrackRGenomicDataStreamggwasGO.ddbGSE142512HaploBreedRhcocenahmagmaRiconicinferRecomIntegratedLearnerkarioCaSKODAMAlanternLongOmicsTrajloopcityDataloopQTLMagellanNTKmdclustmesamethylTFRmethylTFRAnnotationHg38methylTFRAnnotationMm10mgccaMiCARAMOTLMRCCCMRManalyzeRMsBackendParquetMsExperimentStashmyoRDNANADIAOmicsChronoOmicsLakeOmniCorrorthoRibbonPACEPACMOSDatapanpathAuditpath2pathpawehpdactraceperturbMatchperturbMatchDataPhiSpacePlantTxDbHubpostexportKineticsprolfquaProtein2TissuePscanRPscanRBackgroundsPTMsToPathwaysDataQuickBLASTRAMENreglScatterplotRremartRhyMERPBCsaintexpresssbivarscDonorAuditsceptrescGenePanelsciNOMEscMAGeCKscOverlayscProkaRscSimEvalselexprepRSpaMTPSpaMTPdbSPAROscoreSpatialData.plotspatialDESeqspbtest3spbtest5strainspySTRprofilerRSummarizedHeatmapSwitchClasstewastTEscanRTweedieverseTweedSpotTxDb.Athaliana.Ensembl.TAIR10TxDb.Gmax.JGI.Gmv4TxParq.Hs.gencode.v49WithinHostExperimentwoven

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BreedingExperiment::demoBreeding (BreedingExperiment)CDEnrich::cd_Genesets (data.frame)CDEnrich::demo_all_genes (character)CDEnrich::demo_deg (character)CDEnrich::demo_deg_list (list)CDEnrich::demo_expr (matrix)CDEnrich::demo_group (factor)CDEnrich::demo_rank_apop (numeric)CDEnrich::demo_rank_apop_list (list)CDEnrich::demo_targeted_deg (character)CDEnrich::representative_genes (list)CDEnrich::representative_pathways (data.frame)DEP::DiUbi (data.frame)DEP::DiUbi_ExpDesign (data.frame)DEP::UbiLength (data.frame)DEP::UbiLength_ExpDesign (data.frame)ECLIPSE::post_qc_contigs (tbl_df)ECLIPSE::test_seurat (Seurat)ECLIPSE::test_seurat_with_tcr (Seurat)ECLIPSE::vignette_object (Seurat)epiPortrait::example_se (RangedSummarizedExperiment)epiwraps::exampleDNAme (UnstitchedGPos)epiwraps::exampleESE (EnrichmentSE)epiwraps::geneBodies (GRanges)GeneSCARAB::circa_table_genescarab (data.frame)ggwas::example_gwas (gwas_data)hmagmaR::annotated_genes (data.table)hmagmaR::enhancerRegions (data.frame)hmagmaR::gwas (data.table)hmagmaR::hic (tbl_df)hmagmaR::promoterRegions (data.frame)hmagmaR::regulatoryRegions (data.frame)hmagmaR::snpgeneexon (data.table)hmagmaR::snps (data.table)IntegratedLearner::Franzosa_MAE_train (MultiAssayExperiment)IntegratedLearner::Franzosa_MAE_valid (MultiAssayExperiment)IntegratedLearner::FranzosaE_2019_CuratedMetabolome (data.frame)IntegratedLearner::FranzosaE_2019_CuratedMetadata (data.frame)IntegratedLearner::FranzosaE_2019_CuratedSpeciesProfile (data.frame)IntegratedLearner::FranzosaE_2019_Validation_CuratedMetabolome (data.frame)IntegratedLearner::FranzosaE_2019_Validation_CuratedMetadata (data.frame)IntegratedLearner::FranzosaE_2019_Validation_CuratedSpeciesProfile (data.frame)IntegratedLearner::gene_all (data.frame)IntegratedLearner::mir_all (data.frame)IntegratedLearner::NLIBD (list)IntegratedLearner::NLIBD_MAE (MultiAssayExperiment)IntegratedLearner::pregnancy (list)IntegratedLearner::pregnancy_MAE (MultiAssayExperiment)IntegratedLearner::PRISM (list)IntegratedLearner::PRISM_MAE (MultiAssayExperiment)IntegratedLearner::TCGA_survival_MAE_train (MultiAssayExperiment)IntegratedLearner::TCGA_survival_MAE_valid (MultiAssayExperiment)KODAMA::lymphoma (list)KODAMA::MetRef (list)KODAMA::USA (list)LongOmicsTraj::lot_glucold (LongOmicsTraj)LongOmicsTraj::lot_glucold_clinical (data.frame)LongOmicsTraj::lot_glucold_expression (matrix)LongOmicsTraj::lot_glucold_ots (LongOmicsTraj)loopcityData::GM12878_10KbLoops (GInteractions)loopcityData::GM12878_10KbLoopsChr21 (GInteractions)MagellanNTK::lldata (MultiAssayExperiment)MagellanNTK::lldata1 (MultiAssayExperiment)MagellanNTK::lldata12 (MultiAssayExperiment)MagellanNTK::lldata123 (MultiAssayExperiment)mesa::BSgenome.Hsapiens.NCBI.GRCh38.CpG.distribution (data.frame)mesa::BSgenome.Hsapiens.UCSC.hg19.CpG.distribution (data.frame)mesa::BSgenome.Mmusculus.UCSC.mm10.CpG.distribution (data.frame)mesa::ENCODEbadRegions (GRanges)mesa::exampleMouse (qseaSet)mesa::exampleTumourNormal (qseaSet)mesa::FantomRegions (tbl_df)mesa::gc_hg38_1000kb (data.table)mesa::gc_hg38_500kb (data.table)mesa::gc_hg38_50kb (data.table)mesa::hg19ToHg38.over.chain (Chain)mesa::hg38_450kArrayGR (GRanges)mesa::hg38CpGIslands (GRanges)mesa::hg38UltraStableProbes (GRanges)mesa::map_hg38_1000kb (data.table)mesa::map_hg38_500kb (data.table)mesa::map_hg38_50kb (data.table)mgcca::X1 (data.frame)mgcca::X2 (data.frame)mgcca::X3 (data.frame)MiCARA::example_metadata (data.frame)MiCARA::example_pathways (data.frame)MiCARA::example_taxa (data.frame)MOTL::Lrn (list)MOTL::TL_param (list)MOTL::Trg (list)NADIA::nadia_dia (spectronaut_data)OmniCorr::metadata (data.frame)OmniCorr::Metagenomics (data.frame)OmniCorr::Metatranscriptomics (data.frame)OmniCorr::Transcriptomics (data.frame)path2path::demo_pathways (list)path2path::demo_z (matrix)pdactrace::atlas_metadata (list)pdactrace::default_templates (list)pdactrace::meta_analysis (data.table)pdactrace::pdactrace_data_sources (data.table)pdactrace::pdactrace_external_anchors (data.frame)pdactrace::pdactrace_protein_betas (data.table)pdactrace::pdactrace_reference (data.table)pdactrace::toy_coldata (data.frame)pdactrace::toy_counts (matrix)pdactrace::toy_protein (matrix)postexportKinetics::postexport_example (data.frame)postexportKinetics::postexport_example_truth (data.frame)prolfqua::data_checksummarizationrobust87 (data.frame)prolfqua::data_checksummarizerobust69 (data.frame)prolfqua::data_ionstar (IonstarData)prolfqua::x5463yzwer453bbb (tbl_df)Protein2Tissue::ee_tb (data.frame)Protein2Tissue::plasma_data (data.frame)Protein2Tissue::tissue_map (data.frame)RAMEN::test_covariates (matrix)RAMEN::test_environmental_matrix (matrix)RAMEN::test_genotype_information (data.frame)RAMEN::test_genotype_matrix (matrix)RAMEN::test_methylation_data (data.frame)RAMEN::ultrastable_cpgs (character)reglScatterplotR::reglScatterExample (data.frame)RPBC::haley_gbm_example (SpatialExperiment)sbivar::Vicari (list)sceptre::gene_position_data_frame_grch37 (data.table)sceptre::gene_position_data_frame_grch38 (data.table)sceptre::grna_target_data_frame_highmoi (data.frame)sceptre::highmoi_example_data (list)sceptre::lowmoi_example_data (list)scOverlay::sce_mpnst_example (SingleCellExperiment)scOverlay::sce_overlay_example (SingleCellExperiment)scProkaR::sce1 (SingleCellExperiment)scSimEval::example_batch_info (factor)scSimEval::example_cell_types (factor)scSimEval::example_multiomics (list)scSimEval::example_scatac (list)scSimEval::example_scrna (list)selexprepR::selexprep_public_catalog (DFrame)SpaMTP::adduct_file (data.frame)SpaMTP::reaction_type (data.frame)SwitchClass::CRC_subset (list)tTEscanR::default_tTEscanR_metadata (data.frame)tTEscanR::default_tTEscanR_mRNA_data (data.frame)tTEscanR::default_tTEscanR_tRNA_data (matrix)WithinHostExperiment::example_whe (WithinHostExperiment)woven::woven_example (list)

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BamScaleRbHIVEbppgBreedingExperimentCanvasXpressBiocascadeRCDEnrichcellchatrcellpaintrcircaTimeClinicalVariantRCMEntconsensusRegionsconsensusTADsConvergeRcpgdirectioncpgdirectionDatacrossarrayEWASDEPDgeaHeatmapdmsadrugannotRECLIPSEepiPortraitepiwrapsexposomeSCfaissRfastEmbedRfastPLSgDRplotsGDSAnnotatorGENCODEHubGeneSCARABgeneticumapGeneTrackRGenomicDataStreamggwasGO.ddbGSE142512HaploBreedRhcocenahmagmaRiconicinferRecomIntegratedLearnerkarioCaSKODAMAlanternLongOmicsTrajloopcityDataloopQTLMagellanNTKmdclustmesamethylTFRmethylTFRAnnotationHg38methylTFRAnnotationMm10mgccaMiCARAMOTLMRCCCMRManalyzeRMsBackendParquetMsExperimentStashmyoRDNANADIAOmicsChronoOmicsLakeOmniCorrorthoRibbonPACEPACMOSDatapanpathAuditpath2pathpawehpdactraceperturbMatchperturbMatchDataPhiSpacePlantTxDbHubpostexportKineticsprolfquaProtein2TissuePscanRPscanRBackgroundsPTMsToPathwaysDataQuickBLASTRAMENreglScatterplotRremartRhyMERPBCsaintexpresssbivarscDonorAuditsceptrescGenePanelsciNOMEscMAGeCKscOverlayscProkaRscSimEvalselexprepRSpaMTPSpaMTPdbSPAROscoreSpatialData.plotspatialDESeqspbtest3spbtest5strainspySTRprofilerRSummarizedHeatmapSwitchClasstewastTEscanRTweedieverseTweedSpotTxDb.Athaliana.Ensembl.TAIR10TxDb.Gmax.JGI.Gmv4TxParq.Hs.gencode.v49WithinHostExperimentwoven