Topics › BiocViews › Software › ResearchField
Epigenetics
biocViews- Packages
- 108108 tagged here
- Distinct IPs
- 619a month, median
- Failing builds
- 18of 108 built
- Release
- 3.23Bioconductor now
Packages
PackageDistinct IPsBuildsFirst release
limmaLinear Models for Microarray and Omics Data44,656 distinct IPs a month, build OKfirst in a release 17 May 2004edgeREmpirical Analysis of Digital Gene Expression Data in R31,065 distinct IPs a month, build OKfirst in a release 22 Oct 2008bumphunterBump Hunter3,911 distinct IPs a month, build OKfirst in a release 4 Apr 2013minfiAnalyze Illumina Infinium DNA methylation arrays3,714 distinct IPs a month, build OKfirst in a release 1 Nov 2011variancePartitionQuantify and interpret drivers of variation in multilevel gene expression experiments2,895 distinct IPs a month, build OKfirst in a release 14 Oct 2015DiffBindDifferential Binding Analysis of ChIP-Seq Peak Data2,194 distinct IPs a month, build OKfirst in a release 1 Nov 2011DMRcateMethylation array and sequencing spatial analysis methods1,708 distinct IPs a month, build errorfirst in a release 14 Apr 2014EpiDISHEpigenetic Dissection of Intra-Sample-Heterogeneity1,585 distinct IPs a month, build OKfirst in a release 31 Oct 2017TOASTTools for the analysis of heterogeneous tissues1,274 distinct IPs a month, build OKfirst in a release 30 Oct 2019RnBeadsRnBeads1,065 distinct IPs a month, build OKfirst in a release 17 Apr 2015TCseqTime course sequencing data analysis1,046 distinct IPs a month, build warningsfirst in a release 25 Apr 2017dmrseqDetection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing992 distinct IPs a month, build OKfirst in a release 1 May 2018GOTHiCBinomial test for Hi-C data analysis973 distinct IPs a month, build errorfirst in a release 14 Apr 2014ciceroPredict cis-co-accessibility from single-cell chromatin accessibility data949 distinct IPs a month, build OKfirst in a release 31 Oct 2018ENmixQuality control and analysis tools for Illumina DNA methylation BeadChip944 distinct IPs a month, build OKfirst in a release 17 Apr 2015BEATBEAT - BS-Seq Epimutation Analysis Toolkit870 distinct IPs a month, build OKfirst in a release 14 Apr 2014monaLisaBinned Motif Enrichment Analysis and Visualization865 distinct IPs a month, build OKfirst in a release 27 Oct 2021MethPedA DNA methylation classifier tool for the identification of pediatric brain tumor subtypes855 distinct IPs a month, build OKfirst in a release 4 May 2016chipenrichGene Set Enrichment For ChIP-seq Peak Data816 distinct IPs a month, build OKfirst in a release 15 Oct 2013DEScan2Differential Enrichment Scan 2806 distinct IPs a month, build OKfirst in a release 1 May 2018omicsPrintCross omic genetic fingerprinting804 distinct IPs a month, build errorfirst in a release 1 May 2018dreamletScalable differential expression analysis of single cell transcriptomics datasets with complex study designs780 distinct IPs a month, build OKfirst in a release 25 Oct 2023COCOACoordinate Covariation Analysis779 distinct IPs a month, build OKfirst in a release 31 Oct 2018mCSEAMethylated CpGs Set Enrichment Analysis777 distinct IPs a month, build errorfirst in a release 1 May 2018fCCACfunctional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets774 distinct IPs a month, build OKfirst in a release 18 Oct 2016ChromSCapeAnalysis of single-cell epigenomics datasets with a Shiny App771 distinct IPs a month, build OKfirst in a release 28 Oct 2020metaseqR2An 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 2020MEATMuscle Epigenetic Age Test748 distinct IPs a month, build warningsfirst in a release 28 Apr 2020proActivEstimate Promoter Activity from RNA-Seq data735 distinct IPs a month, build OKfirst in a release 28 Oct 2020sevenCComputational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs734 distinct IPs a month, build OKfirst in a release 1 May 2018epigraHMMEpigenomic R-based analysis with hidden Markov models729 distinct IPs a month, build warningsfirst in a release 20 May 2021omicRexposomeExposome and omic data associatin and integration analysis722 distinct IPs a month, build OKfirst in a release 31 Oct 2017methylInheritancePermutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect722 distinct IPs a month, build OKfirst in a release 25 Apr 2017nullrangesGeneration of null ranges via bootstrapping or covariate matching720 distinct IPs a month, build OKfirst in a release 27 Oct 2021MIRAMethylation-Based Inference of Regulatory Activity718 distinct IPs a month, build OKfirst in a release 31 Oct 2017planetPlacental DNA methylation analysis tools717 distinct IPs a month, build OKfirst in a release 20 May 2021ChicagoCHiCAGO: Capture Hi-C Analysis of Genomic Organization709 distinct IPs a month, build OKfirst in a release 4 May 2016recountmethylationAccess and analyze public DNA methylation array data compilations706 distinct IPs a month, build OKfirst in a release 28 Oct 2020easierEstimate Systems Immune Response from RNA-seq data696 distinct IPs a month, build OKfirst in a release 27 Oct 2021OMICsPCAAn R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples696 distinct IPs a month, build OKfirst in a release 31 Oct 2018REMPRepetitive Element Methylation Prediction695 distinct IPs a month, build errorfirst in a release 25 Apr 2017srnadiffFinding differentially expressed unannotated genomic regions from RNA-seq data689 distinct IPs a month, build warningsfirst in a release 1 May 2018methimputeImputation-guided re-construction of complete methylomes from WGBS data682 distinct IPs a month, build warningsfirst in a release 31 Oct 2017zenithGene set analysis following differential expression using linear (mixed) modeling with dream675 distinct IPs a month, build warningsfirst in a release 2 Nov 2022InTADSearch for correlation between epigenetic signals and gene expression in TADs667 distinct IPs a month, build OKfirst in a release 1 May 2018NanoMethVizVisualise methylation data from Oxford Nanopore sequencing662 distinct IPs a month, build OKfirst in a release 28 Oct 2020methylSigMethylSig: Differential Methylation Testing for WGBS and RRBS Data651 distinct IPs a month, build OKfirst in a release 28 Apr 2020methInheritSimSimulating Whole-Genome Inherited Bisulphite Sequencing Data650 distinct IPs a month, build OKfirst in a release 31 Oct 2017pathwayPCAIntegrative Pathway Analysis with Modern PCA Methodology and Gene Selection634 distinct IPs a month, build OKfirst in a release 3 May 2019idr2dIrreproducible Discovery Rate for Genomic Interactions Data633 distinct IPs a month, build OKfirst in a release 30 Oct 2019epialleleRFast, Accurate, Epiallele-Aware Methylation Caller and Reporter631 distinct IPs a month, build OKfirst in a release 20 May 2021methylscaperVisualization of Methylation Data630 distinct IPs a month, build OKfirst in a release 20 May 2021EpiMixEpiMix: an integrative tool for the population-level analysis of DNA methylation620 distinct IPs a month, build OKfirst in a release 2 Nov 2022msgbsRmsgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions619 distinct IPs a month, build OKfirst in a release 25 Apr 2017coMethDMRAccurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies618 distinct IPs a month, build timeoutfirst in a release 27 Apr 2022cbafAutomated functions for comparing various omic data from cbioportal.org612 distinct IPs a month, build OKfirst in a release 31 Oct 2017ramrDetection of Rare Aberrantly Methylated Regions in Array and NGS Data602 distinct IPs a month, build OKfirst in a release 20 May 2021EpiCompareComparison, Benchmarking & QC of Epigenomic Datasets597 distinct IPs a month, build OKfirst in a release 27 Apr 2022Motif2SiteDetect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions592 distinct IPs a month, build OKfirst in a release 27 Apr 2022AlphaBetaComputational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants592 distinct IPs a month, build OKfirst in a release 30 Oct 2019xcorexcore expression regulators inference590 distinct IPs a month, build OKfirst in a release 27 Apr 2022TRESSToolbox for mRNA epigenetics sequencing analysis581 distinct IPs a month, build OKfirst in a release 27 Oct 2021CTdataData companion to CTexploreR581 distinct IPs a month, build timeoutfirst in a release 26 Apr 2023rnaEditrStatistical analysis of RNA editing sites and hyper-editing regions579 distinct IPs a month, build warningsfirst in a release 28 Oct 2020mitchMulti-Contrast Gene Set Enrichment Analysis564 distinct IPs a month, build OKfirst in a release 28 Apr 2020scMETBayesian modelling of cell-to-cell DNA methylation heterogeneity564 distinct IPs a month, build errorfirst in a release 2 Nov 2022CTexploreRExplores Cancer Testis Genes557 distinct IPs a month, build timeoutfirst in a release 1 May 2024MethRegAssessing the regulatory potential of DNA methylation regions or sites on gene transcription557 distinct IPs a month, build errorfirst in a release 28 Oct 2020epidecodeRepidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation556 distinct IPs a month, build OKfirst in a release 20 May 2021cliProfilerA package for the CLIP data visualization555 distinct IPs a month, build OKfirst in a release 27 Oct 2021m6Aboostm6Aboost554 distinct IPs a month, build OKfirst in a release 27 Oct 2021MAGARMAGAR: 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 2021nuCposAn R package for prediction of nucleosome positions532 distinct IPs a month, build OKfirst in a release 31 Oct 2018BiFETBias-free Footprint Enrichment Test532 distinct IPs a month, build OKfirst in a release 1 May 2018SOMNiBUSSmooth modeling of bisulfite sequencing530 distinct IPs a month, build OKfirst in a release 20 May 2021roastgsaRotation based gene set analysis509 distinct IPs a month, build OKfirst in a release 25 Oct 2023MIRitIntegrate microRNA and gene expression to decipher pathway complexity499 distinct IPs a month, build errorfirst in a release 1 May 2024PoDCallPositive Droplet Calling for DNA Methylation Droplet Digital PCR485 distinct IPs a month, build OKfirst in a release 20 May 2021dinoRDifferential NOMe-seq analysis476 distinct IPs a month, build OKfirst in a release 1 May 2024GApredictionPrediction of gestational age with Illumina HumanMethylation450 data471 distinct IPs a month, build OKfirst in a release 18 Oct 2016netboostNetwork Analysis Supported by Boosting470 distinct IPs a month, build OKfirst in a release 3 May 2019ISoLDEIntegrative Statistics of alleLe Dependent Expression467 distinct IPs a month, build warningsfirst in a release 4 May 2016BPRMethModel higher-order methylation profiles464 distinct IPs a month, build errorfirst in a release 18 Oct 2016G4SNVHunterEvaluating SNV-Induced Disruption of G-Quadruplex Structures449 distinct IPs a month, build warningsfirst in a release 16 Apr 2025TENETR package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors444 distinct IPs a month, build OKfirst in a release 16 Apr 2025vmrseqProbabilistic Modeling of Single-cell Methylation Heterogeneity438 distinct IPs a month, build OKfirst in a release 16 Apr 2025crumblrCount ratio uncertainty modeling base linear regression430 distinct IPs a month, build OKfirst in a release 16 Apr 2025tidyexposomicsIntegrated Exposure-Omics Analysis Powered by Tidy Principles413 distinct IPs a month, build OKfirst in a release 29 Apr 2026HiCaptuReHiCaptuRe: Manipulating and integrating Capture Hi-C data407 distinct IPs a month, build OKfirst in a release 30 Oct 2025damidBindDifferential Binding and Expression Analysis for DamID-seq Data405 distinct IPs a month, build OKfirst in a release 29 Apr 2026mistDifferential Methylation Analysis for scDNAm Data398 distinct IPs a month, build OKfirst in a release 16 Apr 2025gVennProportional Venn and UpSet Diagrams for Gene Sets and Genomic Regions397 distinct IPs a month, build errorfirst in a release 30 Oct 2025SPICEYCalculates cell type specificity from single cell data390 distinct IPs a month, build OKfirst in a release 30 Oct 2025Site2TargetAn R package to associate peaks and target genes386 distinct IPs a month, build OKfirst in a release 16 Apr 2025MelissaBayesian clustering and imputationa of single cell methylomes373 distinct IPs a month, built, not publishedfirst in a release 3 May 2019MotifPeekerBenchmarking Epigenomic Profiling Methods Using Motif Enrichment366 distinct IPs a month, build OKfirst in a release 16 Apr 2025SingleMoleculeFootprintingAnalysis tools for Single Molecule Footprinting (SMF) data359 distinct IPs a month, build errorfirst in a release 20 May 2021decemediphierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylome346 distinct IPs a month, build errorfirst in a release 29 Apr 2026chipenrich.dataCompanion package to chipenrich338 distinct IPs a month, build warningsfirst in a release 15 Oct 2013knowYourCGFunctional analysis of DNA methylome datasets338 distinct IPs a month, build OKfirst in a release 1 May 2024EpipwREfficient Power Analysis for EWAS with Continuous or Binary Outcomes328 distinct IPs a month, build OKfirst in a release 30 Oct 2024RBedMethylDisk-backed Representation of ONT bedMethyl Files316 distinct IPs a month, build OKfirst in a release 29 Apr 2026atacInferCnvCall CNV from single cell ATAC-seq data based on InferCNV adaptation285 distinct IPs a month, build OKfirst in a release 29 Apr 2026betterChromVARImproved ChromVAR (Chromatin Variation Across Regions)285 distinct IPs a month, build OKfirst in a release 29 Apr 2026cfToolsInformatics Tools for Cell-Free DNA Study269 distinct IPs a month, build errorfirst in a release 26 Apr 2023epiRomicsEpigenomic Analysis Package Built for R (epiRomics)265 distinct IPs a month, build OKfirst in a release 29 Apr 2026HiSpaRHierarchical Inference of Spatial Positions from Hi-C Data238 distinct IPs a month, build OKfirst in a release 29 Apr 2026spatzieIdentification of enriched motif pairs from chromatin interaction data217 distinct IPs a month, build errorfirst in a release 27 Oct 2021
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