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DataImport

biocViews
Packages
349349 tagged here
Distinct IPs
673a month, median
Failing builds
55of 346 built
Release
3.23Bioconductor now

Bioconductor pageSourceIn the package list

Packages

PackageDistinct IPsBuildsFirst release

BiostringsEfficient manipulation of biological strings57,909 distinct IPs a month, build warningsfirst in a release 17 May 2004limmaLinear Models for Microarray and Omics Data44,656 distinct IPs a month, build OKfirst in a release 17 May 2004ggtreean R package for visualization of tree and annotation data34,055 distinct IPs a month, build OKfirst in a release 17 Apr 2015treeioBase Classes and Functions for Phylogenetic Tree Input and Output31,558 distinct IPs a month, build OKfirst in a release 25 Apr 2017RsamtoolsBinary alignment (BAM), FASTA, variant call (BCF), and tabix file import30,396 distinct IPs a month, build warningsfirst in a release 28 Oct 2009BiocFileCacheManage Files Across Sessions29,516 distinct IPs a month, build errorfirst in a release 25 Apr 2017RhtslibHTSlib high-throughput sequencing library as an R package27,697 distinct IPs a month, build OKfirst in a release 17 Apr 2015rhdf5R Interface to HDF527,153 distinct IPs a month, build warningsfirst in a release 5 Jan 2001GenomicAlignmentsRepresentation and manipulation of short genomic alignments26,583 distinct IPs a month, build OKfirst in a release 14 Apr 2014UCSC.utilsLow-level utilities to retrieve data from the UCSC Genome Browser26,272 distinct IPs a month, build OKfirst in a release 1 May 2024rhdf5filtersHDF5 Compression Filters25,866 distinct IPs a month, build OKfirst in a release 28 Apr 2020rtracklayerR interface to genome annotation files and the UCSC genome browser25,599 distinct IPs a month, build warningsfirst in a release 1 May 2008SingleCellExperimentS4 Classes for Single Cell Data23,697 distinct IPs a month, build OKfirst in a release 31 Oct 2017BiocIOStandard Input and Output for Bioconductor Packages22,645 distinct IPs a month, build OKfirst in a release 28 Oct 2020beachmatCompiling Bioconductor to Handle Each Matrix Type21,592 distinct IPs a month, build warningsfirst in a release 31 Oct 2017HDF5ArrayHDF5 datasets as array-like objects in R19,803 distinct IPs a month, build OKfirst in a release 4 May 2016assortheadAssorted Header-Only C++ Libraries18,833 distinct IPs a month, build OKfirst in a release 30 Oct 2024GEOqueryGet data from NCBI Gene Expression Omnibus (GEO)15,499 distinct IPs a month, build errorfirst in a release 27 Apr 2006AnnotationHubClient to access AnnotationHub resources15,331 distinct IPs a month, build OKfirst in a release 4 Apr 2013h5mreadA fast HDF5 reader14,613 distinct IPs a month, build OKfirst in a release 16 Apr 2025scuttleLegacy Utilities for Single-Cell RNA-Seq Analysis13,591 distinct IPs a month, build warningsfirst in a release 28 Oct 2020scaterSingle-Cell Analysis Toolkit for Gene Expression Data in R11,874 distinct IPs a month, build warningsfirst in a release 4 May 2016ExperimentHubClient to access ExperimentHub resources10,831 distinct IPs a month, build warningsfirst in a release 15 Oct 2013affyioTools for parsing Affymetrix data files10,300 distinct IPs a month, build warningsfirst in a release 27 Apr 2006SpatialExperimentS4 Class for Spatially Resolved -omics Data10,258 distinct IPs a month, build OKfirst in a release 28 Oct 2020VariantAnnotationAnnotation of Genetic Variants9,771 distinct IPs a month, build warningsfirst in a release 1 Nov 2011ShortReadFASTQ input and manipulation7,812 distinct IPs a month, build errorfirst in a release 1 May 2008biomformatAn interface package for the BIOM file format7,699 distinct IPs a month, build OKfirst in a release 4 May 2016txdbmakerTools for making TxDb objects from genomic annotations5,695 distinct IPs a month, build errorfirst in a release 1 May 2024alabaster.baseSave Bioconductor Objects to File5,660 distinct IPs a month, build OKfirst in a release 26 Apr 2023tximportImport and summarize transcript-level estimates for transcript- and gene-level analysis5,528 distinct IPs a month, build OKfirst in a release 4 May 2016alabaster.matrixLoad and Save Artifacts from File5,380 distinct IPs a month, build OKfirst in a release 26 Apr 2023mzRparser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)5,344 distinct IPs a month, build warningsfirst in a release 1 Nov 2011alabaster.rangesLoad and Save Ranges-related Artifacts from File5,301 distinct IPs a month, build OKfirst in a release 26 Apr 2023alabaster.seLoad and Save SummarizedExperiments from File5,281 distinct IPs a month, build OKfirst in a release 26 Apr 2023MSnbaseBase Functions and Classes for Mass Spectrometry and Proteomics5,179 distinct IPs a month, build errorfirst in a release 14 Apr 2011alabaster.schemasSchemas for the Alabaster Framework5,166 distinct IPs a month, build OKfirst in a release 26 Apr 2023gypsumInterface to the gypsum REST API5,099 distinct IPs a month, build OKfirst in a release 1 May 2024DECIPHERTools for curating, analyzing, and manipulating biological sequences4,603 distinct IPs a month, build OKfirst in a release 1 Nov 2011mzIDAn mzIdentML parser for R4,399 distinct IPs a month, build OKfirst in a release 15 Oct 2013monocleClustering, differential expression, and trajectory analysis for single- cell RNA-Seq4,347 distinct IPs a month, build OKfirst in a release 14 Oct 2014illuminaioParsing Illumina Microarray Output Files4,127 distinct IPs a month, build OKfirst in a release 4 Apr 2013zellkonverterConversion Between scRNA-seq Objects4,116 distinct IPs a month, build errorfirst in a release 28 Oct 2020oligoPreprocessing tools for oligonucleotide arrays3,920 distinct IPs a month, build OKfirst in a release 18 May 2005DropletUtilsUtilities for Handling Single-Cell Droplet Data3,818 distinct IPs a month, build warningsfirst in a release 1 May 2018minfiAnalyze Illumina Infinium DNA methylation arrays3,714 distinct IPs a month, build OKfirst in a release 1 Nov 2011cytolibC++ infrastructure for representing and interacting with the gated cytometry data3,644 distinct IPs a month, build warningsfirst in a release 31 Oct 2017gdsfmtR Interface to CoreArray Genomic Data Structure (GDS) Files3,191 distinct IPs a month, build OKfirst in a release 14 Oct 2014affxparserAffymetrix File Parsing SDK3,098 distinct IPs a month, build errorfirst in a release 14 Oct 2005miaMicrobiome analysis2,796 distinct IPs a month, build timeoutfirst in a release 20 May 2021flowWorkspaceInfrastructure for representing and interacting with gated and ungated cytometry data sets.2,533 distinct IPs a month, build warningsfirst in a release 1 Nov 2011CNErCNE Detection and Visualization2,496 distinct IPs a month, build warningsfirst in a release 14 Apr 2014OmnipathROmniPath web service client and more2,421 distinct IPs a month, build timeoutfirst in a release 30 Oct 2019tximetaTranscript Quantification Import with Automatic Metadata2,337 distinct IPs a month, build OKfirst in a release 31 Oct 2018systemPipeRsystemPipeR: A Multipurpose Workflow Management System for Reproducible Data Analysis2,235 distinct IPs a month, build OKfirst in a release 14 Oct 2014MsExperimentInfrastructure for Mass Spectrometry Experiments2,170 distinct IPs a month, build OKfirst in a release 2 Nov 2022bamsignalsExtract read count signals from bam files2,024 distinct IPs a month, build OKfirst in a release 17 Apr 2015celdaCEllular Latent Dirichlet Allocation2,011 distinct IPs a month, build timeoutfirst in a release 3 May 2019universalmotifImport, Modify, and Export Motifs with R1,968 distinct IPs a month, build OKfirst in a release 31 Oct 2018openCytoHierarchical Gating Pipeline for flow cytometry data1,843 distinct IPs a month, build warningsfirst in a release 15 Oct 2013karyoploteRPlot customizable linear genomes displaying arbitrary data1,822 distinct IPs a month, build OKfirst in a release 25 Apr 2017dittoSeqUser Friendly Single-Cell and Bulk RNA Sequencing Visualization1,760 distinct IPs a month, build OKfirst in a release 28 Apr 2020GenomicDataCommonsNIH / NCI Genomic Data Commons Access1,716 distinct IPs a month, build errorfirst in a release 25 Apr 2017DMRcateMethylation array and sequencing spatial analysis methods1,708 distinct IPs a month, build errorfirst in a release 14 Apr 2014alabaster.sceLoad and Save SingleCellExperiment from File1,701 distinct IPs a month, build OKfirst in a release 26 Apr 2023ChemmineRCheminformatics Toolkit for R1,650 distinct IPs a month, build errorfirst in a release 22 Oct 2008GenomicFilesDistributed computing by file or by range1,613 distinct IPs a month, build OKfirst in a release 14 Apr 2014motifStackPlot stacked logos for single or multiple DNA, RNA and amino acid sequence1,562 distinct IPs a month, build OKfirst in a release 3 Oct 2012anndataRAnnData interoperability in R1,512 distinct IPs a month, build OKfirst in a release 30 Oct 2025TCGAutilsTCGA utility functions for data management1,498 distinct IPs a month, build OKfirst in a release 1 May 2018CytoMLA GatingML Interface for Cross Platform Cytometry Data Sharing1,404 distinct IPs a month, build warningsfirst in a release 18 Oct 2016chipseqchipseq: A package for analyzing chipseq data1,404 distinct IPs a month, build warningsfirst in a release 22 Oct 2008recount3Explore and download data from the recount3 project1,386 distinct IPs a month, build errorfirst in a release 28 Oct 2020AnnotationHubDataTransform public data resources into Bioconductor Data Structures1,330 distinct IPs a month, build warningsfirst in a release 4 Apr 2013R4RNAAn R package for RNA visualization and analysis1,243 distinct IPs a month, build OKfirst in a release 4 May 2016MsBackendMgfMass Spectrometry Data Backend for Mascot Generic Format (mgf) Files1,236 distinct IPs a month, build OKfirst in a release 20 May 2021GenomicInteractionsUtilities for handling genomic interaction data1,211 distinct IPs a month, build OKfirst in a release 14 Oct 2014recountExplore and download data from the recount project1,203 distinct IPs a month, build timeoutfirst in a release 18 Oct 2016rpxR Interface to the ProteomeXchange Repository1,194 distinct IPs a month, build OKfirst in a release 14 Apr 2014IsoformSwitchAnalyzeRIdentify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data1,183 distinct IPs a month, build OKfirst in a release 31 Oct 2017hparHuman Protein Atlas in R1,157 distinct IPs a month, build OKfirst in a release 3 Oct 2012BayesSpaceClustering and Resolution Enhancement of Spatial Transcriptomes1,134 distinct IPs a month, build warningsfirst in a release 28 Oct 2020aCGHClasses and functions for Array Comparative Genomic Hybridization data1,106 distinct IPs a month, build OKfirst in a release 17 May 2004ExperimentHubDataAdd resources to ExperimentHub1,098 distinct IPs a month, build warningsfirst in a release 4 May 2016scmapA tool for unsupervised projection of single cell RNA-seq data1,096 distinct IPs a month, build OKfirst in a release 31 Oct 2017CATALYSTCytometry dATa anALYSis Tools1,094 distinct IPs a month, build OKfirst in a release 25 Apr 2017SRAdbA compilation of metadata from NCBI SRA and tools1,088 distinct IPs a month, build OKfirst in a release 23 Apr 2010cmapRCMap Tools in R1,085 distinct IPs a month, build OKfirst in a release 28 Apr 2020MSstatsConvertImport Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format1,078 distinct IPs a month, build OKfirst in a release 28 Oct 2020BioNetRoutines for the functional analysis of biological networks1,074 distinct IPs a month, build OKfirst in a release 18 Oct 2010RnBeadsRnBeads1,065 distinct IPs a month, build OKfirst in a release 17 Apr 2015makecdfenvCDF Environment Maker1,064 distinct IPs a month, build warningsfirst in a release 17 May 2004deepSNVDetection of subclonal SNVs in deep sequencing data.1,047 distinct IPs a month, build OKfirst in a release 2 Apr 2012codelinkManipulation of Codelink microarray data1,037 distinct IPs a month, build OKfirst in a release 27 Apr 2006GeneRegionScanGeneRegionScan1,037 distinct IPs a month, build OKfirst in a release 21 Apr 2009NanoStringNCToolsNanoString nCounter Tools1,033 distinct IPs a month, build OKfirst in a release 20 May 2021pumaPropagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)1,033 distinct IPs a month, build OKfirst in a release 26 Apr 2007singleCellTKComprehensive and Interactive Analysis of Single Cell RNA-Seq Data1,032 distinct IPs a month, build warningsfirst in a release 1 May 2018ArrayExpressAccess the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet1,030 distinct IPs a month, build OKfirst in a release 1 May 2008RTCGAThe Cancer Genome Atlas Data Integration1,028 distinct IPs a month, build errorfirst in a release 14 Oct 2015cytomapperVisualization of highly multiplexed imaging data in R1,007 distinct IPs a month, build OKfirst in a release 28 Apr 2020LoomExperimentLoomExperiment container1,001 distinct IPs a month, build OKfirst in a release 31 Oct 2018HubPubUtilities to create and use Bioconductor Hubs996 distinct IPs a month, build OKfirst in a release 20 May 2021RqcQuality Control Tool for High-Throughput Sequencing Data990 distinct IPs a month, build OKfirst in a release 14 Oct 2014matterOut-of-core statistical computing and signal processing988 distinct IPs a month, build OKfirst in a release 18 Oct 2016affylmGUIGUI for limma Package with Affymetrix Microarrays967 distinct IPs a month, build OKfirst in a release 17 May 2004segmentSeqMethods for identifying small RNA loci from high-throughput sequencing data950 distinct IPs a month, build OKfirst in a release 23 Apr 2010nucleRNucleosome positioning package for R949 distinct IPs a month, build warningsfirst in a release 1 Nov 2011podkatPosition-Dependent Kernel Association Test946 distinct IPs a month, build OKfirst in a release 17 Apr 2015ENmixQuality control and analysis tools for Illumina DNA methylation BeadChip944 distinct IPs a month, build OKfirst in a release 17 Apr 2015muscleMultiple Sequence Alignment with MUSCLE935 distinct IPs a month, build warningsfirst in a release 17 Apr 2015fmcsRMismatch Tolerant Maximum Common Substructure Searching931 distinct IPs a month, build errorfirst in a release 3 Oct 2012ORFikOpen Reading Frames in Genomics925 distinct IPs a month, build errorfirst in a release 1 May 2018rexposomeExposome exploration and outcome data analysis924 distinct IPs a month, build warningsfirst in a release 31 Oct 2017HTqPCRAutomated analysis of high-throughput qPCR data912 distinct IPs a month, build OKfirst in a release 28 Oct 2009limmaGUIGUI for limma Package With Two Color Microarrays905 distinct IPs a month, build OKfirst in a release 17 May 2004GeomxToolsNanoString GeoMx Tools904 distinct IPs a month, build OKfirst in a release 20 May 2021recoupAn R package for the creation of complex genomic profile plots901 distinct IPs a month, build OKfirst in a release 4 May 2016traseRGWAS trait-associated SNP enrichment analyses in genomic intervals900 distinct IPs a month, build OKfirst in a release 14 Oct 2015CAGEfightRAnalysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor890 distinct IPs a month, build OKfirst in a release 1 May 2018imcRtoolsMethods for imaging mass cytometry data analysis888 distinct IPs a month, build warningsfirst in a release 27 Oct 2021ChemmineOBR interface to a subset of OpenBabel functionalities878 distinct IPs a month, build errorfirst in a release 15 Oct 2013normrNormalization and difference calling in ChIP-seq data866 distinct IPs a month, build warningsfirst in a release 18 Oct 2016R453Plus1ToolboxA package for importing and analyzing data from Roche's Genome Sequencer System862 distinct IPs a month, build OKfirst in a release 18 Oct 2010ggkeggAnalyzing and visualizing KEGG information using the grammar of graphics861 distinct IPs a month, build errorfirst in a release 25 Oct 2023cogenaco-expressed gene-set enrichment analysis850 distinct IPs a month, build warningsfirst in a release 17 Apr 2015TRONCOTRONCO, an R package for TRanslational ONCOlogy844 distinct IPs a month, build OKfirst in a release 17 Apr 2015genomeIntervalsOperations on genomic intervals834 distinct IPs a month, build warningsfirst in a release 21 Apr 2009GuitarGuitar829 distinct IPs a month, build OKfirst in a release 14 Oct 2015RarrRead Zarr Files in R823 distinct IPs a month, build errorfirst in a release 26 Apr 2023ctcCluster and Tree Conversion.822 distinct IPs a month, build OKfirst in a release 17 May 2004HiCBricksFramework for Storing and Accessing Hi-C Data Through HDF Files821 distinct IPs a month, build OKfirst in a release 31 Oct 2018IONiseRQuality Assessment Tools for Oxford Nanopore MinION data812 distinct IPs a month, build errorfirst in a release 14 Oct 2015CTDquerierPackage for CTDbase data query, visualization and downstream analysis812 distinct IPs a month, build warningsfirst in a release 1 May 2018OTUbaseProvides structure and functions for the analysis of OTU data806 distinct IPs a month, build OKfirst in a release 18 Oct 2010DAPARTools for the Differential Analysis of Proteins Abundance with R804 distinct IPs a month, build OKfirst in a release 14 Oct 2015RcpiMolecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery799 distinct IPs a month, build OKfirst in a release 14 Apr 2014biscuiteerConvenience Functions for Biscuit796 distinct IPs a month, build timeoutfirst in a release 30 Oct 2019HelloRangesIntroduce *Ranges to bedtools users783 distinct IPs a month, build OKfirst in a release 18 Oct 2016MsBackendMspMass Spectrometry Data Backend for NIST msp Files781 distinct IPs a month, build OKfirst in a release 27 Apr 2022ASICSAutomatic Statistical Identification in Complex Spectra780 distinct IPs a month, build warningsfirst in a release 1 May 2018profileplyrVisualization and annotation of read signal over genomic ranges with profileplyr771 distinct IPs a month, build errorfirst in a release 3 May 2019metaseqR2An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms764 distinct IPs a month, build errorfirst in a release 28 Apr 2020TVTBTVTB: The VCF Tool Box758 distinct IPs a month, build OKfirst in a release 18 Oct 2016StructuralVariantAnnotationVariant annotations for structural variants758 distinct IPs a month, build OKfirst in a release 3 May 2019biobroomTurn Bioconductor objects into tidy data frames755 distinct IPs a month, build errorfirst in a release 14 Oct 2015ReadqPCRRead qPCR data752 distinct IPs a month, build OKfirst in a release 1 Nov 2011HELPTools for HELP data analysis745 distinct IPs a month, build OKfirst in a release 22 Oct 2008CONFESSCell OrderiNg by FluorEScence Signal743 distinct IPs a month, build warningsfirst in a release 4 May 2016bigmelonIllumina methylation array analysis for large experiments743 distinct IPs a month, build warningsfirst in a release 18 Oct 2016edgeExtraction of Differential Gene Expression742 distinct IPs a month, build OKfirst in a release 17 Apr 2015Basic4CseqBasic4Cseq: an R/Bioconductor package for analyzing 4C-seq data738 distinct IPs a month, build OKfirst in a release 14 Apr 2014sevenCComputational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs734 distinct IPs a month, build OKfirst in a release 1 May 2018DoschedaA DownStream Chemo-Proteomics Analysis Pipeline729 distinct IPs a month, build OKfirst in a release 31 Oct 2017ChIPanalyserChIPanalyser: Predicting Transcription Factor Binding Sites722 distinct IPs a month, build OKfirst in a release 31 Oct 2017scPipePipeline for single cell multi-omic data pre-processing719 distinct IPs a month, build OKfirst in a release 31 Oct 2017AlpsNMRAutomated spectraL Processing System for NMR718 distinct IPs a month, build errorfirst in a release 28 Oct 2020qPLEXanalyzerTools for quantitative proteomics data analysis717 distinct IPs a month, build OKfirst in a release 31 Oct 2018periodicDNASet of tools to identify periodic occurrences of k-mers in DNA sequences712 distinct IPs a month, build warningsfirst in a release 28 Oct 2020memesmotif matching, comparison, and de novo discovery using the MEME Suite709 distinct IPs a month, build warningsfirst in a release 20 May 2021RBioFormatsR interface to Bio-Formats708 distinct IPs a month, build OKfirst in a release 26 Apr 2023flowSpecsTools for processing of high-dimensional cytometry data708 distinct IPs a month, build OKfirst in a release 30 Oct 2019sevenbridgesSeven Bridges Platform API Client and Common Workflow Language Tool Builder in R707 distinct IPs a month, build OKfirst in a release 4 May 2016SpanielSpatial Transcriptomics Analysis703 distinct IPs a month, build OKfirst in a release 30 Oct 2019bugsigdbrR-side access to published microbial signatures from BugSigDB702 distinct IPs a month, build OKfirst in a release 27 Oct 2021TENxIOImport methods for 10X Genomics files701 distinct IPs a month, build OKfirst in a release 2 Nov 2022ModstringsWorking with modified nucleotide sequences701 distinct IPs a month, build OKfirst in a release 3 May 2019AMARETTORegulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression700 distinct IPs a month, build warningsfirst in a release 3 May 2019autonomicsUnified Statistical Modeling of Omics Data698 distinct IPs a month, build errorfirst in a release 20 May 2021REMPRepetitive Element Methylation Prediction695 distinct IPs a month, build errorfirst in a release 25 Apr 2017QSutilsQuasispecies Diversity678 distinct IPs a month, build OKfirst in a release 31 Oct 2018bioassayRCross-target analysis of small molecule bioactivity676 distinct IPs a month, build OKfirst in a release 15 Oct 2013tRNAscanImportImporting a tRNAscan-SE result file as GRanges object674 distinct IPs a month, build OKfirst in a release 1 May 2018CopyNumberPlotsCreate Copy-Number Plots using karyoploteR functionality674 distinct IPs a month, build OKfirst in a release 3 May 2019MANORCGH Micro-Array NORmalization673 distinct IPs a month, build OKfirst in a release 14 Oct 2005scDatavizscDataviz: single cell dataviz and downstream analyses673 distinct IPs a month, build OKfirst in a release 28 Oct 2020schexHexbin plots for single cell omics data670 distinct IPs a month, build warningsfirst in a release 30 Oct 2019biodbBiodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases669 distinct IPs a month, build warningsfirst in a release 20 May 2021Scale4CScale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data668 distinct IPs a month, build OKfirst in a release 31 Oct 2017scGPSA complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)668 distinct IPs a month, build OKfirst in a release 30 Oct 2019BgeeDBAnnotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology668 distinct IPs a month, build OKfirst in a release 4 May 2016BindingSiteFinderBinding site defintion based on iCLIP data666 distinct IPs a month, build OKfirst in a release 27 Oct 2021flowTimeAnnotation and analysis of biological dynamical systems using flow cytometry663 distinct IPs a month, build OKfirst in a release 25 Apr 2017NanoMethVizVisualise methylation data from Oxford Nanopore sequencing662 distinct IPs a month, build OKfirst in a release 28 Oct 2020DegNormDegNorm: degradation normalization for RNA-seq data659 distinct IPs a month, build OKfirst in a release 28 Oct 2020cummeRbundAnalysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.658 distinct IPs a month, build errorfirst in a release 1 Nov 2011ProteoDiscoGeneration of customized protein variant databases from genomic variants, splice-junctions and manual sequences658 distinct IPs a month, build warningsfirst in a release 27 Oct 2021ISAnalyticsAnalyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies658 distinct IPs a month, build OKfirst in a release 28 Oct 2020SPIATSpatial Image Analysis of Tissues655 distinct IPs a month, build OKfirst in a release 2 Nov 2022StructstringsImplementation of the dot bracket annotations with Biostrings652 distinct IPs a month, build OKfirst in a release 3 May 2019eiRAccelerated similarity searching of small molecules651 distinct IPs a month, build errorfirst in a release 4 Apr 2013rhdf5clientAccess HDF5 content from HDF Scalable Data Service648 distinct IPs a month, build OKfirst in a release 31 Oct 2017BaseSpaceRR SDK for BaseSpace RESTful API648 distinct IPs a month, build warningsfirst in a release 4 Apr 2013FLAMESFLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data647 distinct IPs a month, build errorfirst in a release 27 Oct 2021bandleAn R package for the Bayesian analysis of differential subcellular localisation experiments646 distinct IPs a month, build warningsfirst in a release 27 Apr 2022CNVfilteRIdentifies false positives of CNV calling tools by using SNV calls642 distinct IPs a month, build OKfirst in a release 30 Oct 2019IWTomicsInterval-Wise Testing for Omics Data641 distinct IPs a month, build warningsfirst in a release 25 Apr 2017CardinalIORead and write mass spectrometry imaging files634 distinct IPs a month, build OKfirst in a release 25 Oct 2023geneXtendeROptimized Functional Annotation Of ChIP-seq Data631 distinct IPs a month, build errorfirst in a release 18 Oct 2016pfamAnalyzeRIdentification of domain isotypes in pfam data631 distinct IPs a month, build OKfirst in a release 26 Apr 2023SCArrayLarge-scale single-cell omics data manipulation with GDS files623 distinct IPs a month, build OKfirst in a release 20 May 2021VisiumIOImport Visium data from the 10X Space Ranger pipeline620 distinct IPs a month, build OKfirst in a release 1 May 2024msgbsRmsgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions619 distinct IPs a month, build OKfirst in a release 25 Apr 2017svaRetroRetrotransposed transcript detection from structural variants619 distinct IPs a month, build warningsfirst in a release 27 Oct 2021TPP2DDetection of ligand-protein interactions from 2D thermal profiles (DLPTP)617 distinct IPs a month, build OKfirst in a release 3 May 2019SCOPEA normalization and copy number estimation method for single-cell DNA sequencing616 distinct IPs a month, build OKfirst in a release 28 Apr 2020chihayaSave Delayed Operations to a HDF5 File615 distinct IPs a month, build OKfirst in a release 26 Apr 2023HiCExperimentBioconductor class for interacting with Hi-C files in R613 distinct IPs a month, build OKfirst in a release 26 Apr 2023tRNAdbImportImporting from tRNAdb and mitotRNAdb as GRanges objects611 distinct IPs a month, build OKfirst in a release 31 Oct 2018GCPtoolsTools for working with gcloud and gsutil608 distinct IPs a month, build OKfirst in a release 30 Oct 2025SpotCleanSpotClean adjusts for spot swapping in spatial transcriptomics data604 distinct IPs a month, build OKfirst in a release 2 Nov 2022RiboDiPADifferential pattern analysis for Ribo-seq data603 distinct IPs a month, build OKfirst in a release 20 May 2021PepsNMRPre-process 1H-NMR FID signals601 distinct IPs a month, build OKfirst in a release 31 Oct 2018systemPipeShinysystemPipeShiny: An Interactive Framework for Workflow Management and Visualization600 distinct IPs a month, build OKfirst in a release 28 Oct 2020iSEEhubiSEE for the Bioconductor ExperimentHub599 distinct IPs a month, build OKfirst in a release 2 Nov 2022SICtoolsFind SNV/Indel differences between two bam files with near relationship594 distinct IPs a month, build warningsfirst in a release 14 Oct 2015LOBSTAHSLipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences593 distinct IPs a month, build OKfirst in a release 18 Oct 2016gemma.RA wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses590 distinct IPs a month, build OKfirst in a release 2 Nov 2022SpatialOmicsOverlaySpatial Overlay for Omic Data from Nanostring GeoMx Data588 distinct IPs a month, build OKfirst in a release 26 Apr 2023SynExtendTools for Comparative Genomics586 distinct IPs a month, build OKfirst in a release 28 Apr 2020megadepthmegadepth: BigWig and BAM related utilities583 distinct IPs a month, build errorfirst in a release 28 Oct 2020KnowSeqKnowSeq R/Bioc package: The Smart Transcriptomic Pipeline583 distinct IPs a month, build errorfirst in a release 30 Oct 2019BSgenomeForgeForge your own BSgenome data package582 distinct IPs a month, build OKfirst in a release 26 Apr 2023CTdataData companion to CTexploreR581 distinct IPs a month, build timeoutfirst in a release 26 Apr 2023beachmat.hdf5beachmat bindings for HDF5-backed matrices581 distinct IPs a month, build OKfirst in a release 25 Oct 2023svaNUMTNUMT detection from structural variant calls581 distinct IPs a month, build OKfirst in a release 27 Oct 2021cytoviewerAn interactive multi-channel image viewer for R579 distinct IPs a month, build OKfirst in a release 26 Apr 2023MuDataSerialization for MultiAssayExperiment Objects579 distinct IPs a month, build OKfirst in a release 27 Apr 2022ExperimentSubsetManages subsets of data with Bioconductor Experiment objects576 distinct IPs a month, build OKfirst in a release 28 Oct 2020faersR interface for FDA Adverse Event Reporting System574 distinct IPs a month, build OKfirst in a release 1 May 2024scCB2CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data571 distinct IPs a month, build OKfirst in a release 28 Oct 2020ncRNAtoolsAn R toolkit for non-coding RNA570 distinct IPs a month, build OKfirst in a release 28 Oct 2020rfaRmAn R interface to the Rfam database570 distinct IPs a month, build errorfirst in a release 28 Apr 2020SimFFPENGS Read Simulator for FFPE Tissue567 distinct IPs a month, build OKfirst in a release 28 Apr 2020brendaDbThe BRENDA Enzyme Database565 distinct IPs a month, build OKfirst in a release 30 Oct 2019mitchMulti-Contrast Gene Set Enrichment Analysis564 distinct IPs a month, build OKfirst in a release 28 Apr 2020ibhInteraction Based Homogeneity for Evaluating Gene Lists560 distinct IPs a month, build OKfirst in a release 14 Apr 2011RtpcaThermal proximity co-aggregation with R560 distinct IPs a month, build OKfirst in a release 28 Oct 2020tanggleVisualization of Phylogenetic Networks559 distinct IPs a month, build OKfirst in a release 27 Oct 2021MethTargetedNGSPerform Methylation Analysis on Next Generation Sequencing Data557 distinct IPs a month, build OKfirst in a release 17 Apr 2015CTexploreRExplores Cancer Testis Genes557 distinct IPs a month, build timeoutfirst in a release 1 May 2024ChIPCompQuantitative comparison of multiple ChIP-seq datasets554 distinct IPs a month, build errorfirst in a release 14 Oct 2015MAGARMAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data554 distinct IPs a month, build OKfirst in a release 20 May 2021snapcountR/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts554 distinct IPs a month, build errorfirst in a release 28 Apr 2020systemPipeToolsTools for data visualization553 distinct IPs a month, build warningsfirst in a release 20 May 2021cbpManagerGenerate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics552 distinct IPs a month, build warningsfirst in a release 20 May 2021mitoClone2Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations551 distinct IPs a month, build warningsfirst in a release 27 Oct 2021RCXR package implementing the Cytoscape Exchange (CX) format546 distinct IPs a month, build OKfirst in a release 27 Apr 2022MassArrayAnalytical Tools for MassArray Data541 distinct IPs a month, build OKfirst in a release 23 Apr 2010sitadelaAn R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms538 distinct IPs a month, build OKfirst in a release 20 May 2021APAlyzerA toolkit for APA analysis using RNA-seq data537 distinct IPs a month, build OKfirst in a release 30 Oct 2019gDRimportPackage for handling the import of dose-response data537 distinct IPs a month, build OKfirst in a release 25 Oct 2023MGnifyRR interface to EBI MGnify metagenomics resource537 distinct IPs a month, build OKfirst in a release 1 May 2024MsBackendMassbankMass Spectrometry Data Backend for MassBank record Files536 distinct IPs a month, build OKfirst in a release 20 May 2021MsBackendSqlSQL-based Mass Spectrometry Data Backend535 distinct IPs a month, build OKfirst in a release 26 Apr 2023simPICFlexible simulation of paired-insertion counts for single-cell ATAC-sequencing data530 distinct IPs a month, build OKfirst in a release 1 May 2024BiocFHIRIllustration of FHIR ingestion and transformation using R528 distinct IPs a month, build OKfirst in a release 2 Nov 2022hdxmsqcAn R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments526 distinct IPs a month, build OKfirst in a release 1 May 2024cytoMEMMarker Enrichment Modeling (MEM)519 distinct IPs a month, build OKfirst in a release 27 Apr 2022rmspcMultiple Sample Peak Calling519 distinct IPs a month, build OKfirst in a release 27 Oct 2021ompBAMC++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files517 distinct IPs a month, build OKfirst in a release 27 Apr 2022MDTSDetection of de novo deletion in targeted sequencing trios515 distinct IPs a month, build OKfirst in a release 1 May 2018iSEEtreeInteractive visualisation for microbiome data514 distinct IPs a month, build OKfirst in a release 30 Oct 2024HicAggRSet of 3D genomic interaction analysis tools512 distinct IPs a month, build warningsfirst in a release 1 May 2024RImmPortRImmPort: Enabling Ready-for-analysis Immunology Research Data512 distinct IPs a month, build OKfirst in a release 4 May 2016flowGateInteractive Cytometry Gating in R511 distinct IPs a month, build OKfirst in a release 26 Apr 2023roastgsaRotation based gene set analysis509 distinct IPs a month, build OKfirst in a release 25 Oct 2023plotGrouperShiny app GUI wrapper for ggplot with built-in statistical analysis507 distinct IPs a month, build OKfirst in a release 31 Oct 2018SpaceTrooperSpaceTrooper performs Quality Control analysis of Image-Based spatial504 distinct IPs a month, build OKfirst in a release 30 Oct 2025cellxgenedpDiscover and Access Single Cell Data Sets in the CELLxGENE Data Portal501 distinct IPs a month, build OKfirst in a release 27 Apr 2022MACSQuantifyRFast treatment of MACSQuantify FACS data500 distinct IPs a month, build OKfirst in a release 30 Oct 2019ndexrNDEx R client library499 distinct IPs a month, build errorfirst in a release 31 Oct 2017geminiGEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens496 distinct IPs a month, build OKfirst in a release 30 Oct 2019cypressCell-Type-Specific Power Assessment495 distinct IPs a month, build OKfirst in a release 1 May 2024CoSIAAn Investigation Across Different Species and Tissues495 distinct IPs a month, build timeoutfirst in a release 26 Apr 2023DspikeInEstimating Absolute Abundance from Microbial Spike-in Controls492 distinct IPs a month, build OKfirst in a release 30 Oct 2025chevreulShinyTools for managing SingleCellExperiment objects as projects491 distinct IPs a month, build OKfirst in a release 16 Apr 2025RcwlPipelinesBioinformatics pipelines based on Rcwl490 distinct IPs a month, build OKfirst in a release 3 May 2019SingleCellAlleleExperimentS4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes488 distinct IPs a month, build warningsfirst in a release 1 May 2024rBLASTR Interface for the Basic Local Alignment Search Tool487 distinct IPs a month, build OKfirst in a release 1 May 2024alabaster.spatialSave and Load Spatial 'Omics Data to/from File486 distinct IPs a month, build OKfirst in a release 26 Apr 2023cellmigRationTrack Cells, Analyze Cell Trajectories and Compute Migration Statistics486 distinct IPs a month, build OKfirst in a release 20 May 2021limpaQuantification and Differential Analysis of Proteomics Data484 distinct IPs a month, build OKfirst in a release 16 Apr 2025SpatialExperimentIORead in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object483 distinct IPs a month, build OKfirst in a release 16 Apr 2025QTLExperimentS4 classes for QTL summary statistics and metadata478 distinct IPs a month, build OKfirst in a release 25 Oct 2023transomics2cytoscapeA tool set for 3D Trans-Omic network visualization with Cytoscape476 distinct IPs a month, build OKfirst in a release 28 Oct 2020easyliftAn R package to perform genomic liftover475 distinct IPs a month, build OKfirst in a release 25 Oct 2023stPipeUpstream pre-processing for Sequencing-Based Spatial Transcriptomics475 distinct IPs a month, build OKfirst in a release 30 Oct 2025chevreulProcessTools for managing SingleCellExperiment objects as projects473 distinct IPs a month, build warningsfirst in a release 16 Apr 2025SCArray.satLarge-scale single-cell RNA-seq data analysis using GDS files and Seurat467 distinct IPs a month, build OKfirst in a release 26 Apr 2023visiumStitchedEnable downstream analysis of Visium capture areas stitched together with Fiji463 distinct IPs a month, build OKfirst in a release 16 Apr 2025basecallQCWorking with Illumina Basecalling and Demultiplexing input and output files463 distinct IPs a month, build errorfirst in a release 25 Apr 2017terraTCGAdataOpenAccess TCGA Data on Terra as MultiAssayExperiment462 distinct IPs a month, build OKfirst in a release 27 Apr 2022MoleculeExperimentPrioritising a molecule-level storage of Spatial Transcriptomics Data459 distinct IPs a month, build OKfirst in a release 26 Apr 2023OSTA.dataOSTA book data459 distinct IPs a month, build errorfirst in a release 16 Apr 2025HoloFoodRR interface to EBI HoloFood resource458 distinct IPs a month, build errorfirst in a release 30 Oct 2024SurfRSurface Protein Prediction and Identification445 distinct IPs a month, build OKfirst in a release 1 May 2024alabaster.maeLoad and Save MultiAssayExperiments444 distinct IPs a month, build OKfirst in a release 26 Apr 2023alabaster.vcfSave and Load Variant Data to/from File444 distinct IPs a month, build OKfirst in a release 26 Apr 2023alabaster.stringSave and Load Biostrings to/from File443 distinct IPs a month, build OKfirst in a release 26 Apr 2023
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10k to 100k25

1k to 10k77

100 to 1k246

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BiocViews 3,785Software 2,618Infrastructure 615DataImport 349DataRepresentation 162GPU 1GUI 68