Topics › BiocViews › Software › StatisticalMethod
Bayesian
biocViews- Packages
- 9191 tagged here
- Distinct IPs
- 603a month, median
- Failing builds
- 9of 91 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 2004DESeq2Differential gene expression analysis based on the negative binomial distribution31,845 distinct IPs a month, build OKfirst in a release 4 Apr 2013edgeREmpirical Analysis of Digital Gene Expression Data in R31,065 distinct IPs a month, build OKfirst in a release 22 Oct 2008pcaMethodsA collection of PCA methods7,214 distinct IPs a month, build OKfirst in a release 4 Oct 2006apeglmApproximate posterior estimation for GLM coefficients7,161 distinct IPs a month, build OKfirst in a release 31 Oct 2017infercnvInfer Copy Number Variation from Single-Cell RNA-Seq Data2,517 distinct IPs a month, build OKfirst in a release 3 May 2019ALDEx2Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account2,311 distinct IPs a month, build OKfirst in a release 14 Oct 2014celdaCEllular Latent Dirichlet Allocation2,011 distinct IPs a month, build warningsfirst in a release 3 May 2019MOFA2Multi-Omics Factor Analysis v21,791 distinct IPs a month, build OKfirst in a release 28 Oct 2020baySeqEmpirical Bayesian analysis of patterns of differential expression in count data1,168 distinct IPs a month, build OKfirst in a release 28 Oct 2009decontXDecontamination of single cell genomics data1,040 distinct IPs a month, build warningsfirst in a release 25 Oct 2023pumaPropagating 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 2007scdeSingle Cell Differential Expression1,033 distinct IPs a month, build warningsfirst in a release 4 May 2016BASiCSBayesian Analysis of Single-Cell Sequencing data995 distinct IPs a month, build OKfirst in a release 31 Oct 2017affylmGUIGUI for limma Package with Affymetrix Microarrays967 distinct IPs a month, build OKfirst in a release 17 May 2004limmaGUIGUI for limma Package With Two Color Microarrays905 distinct IPs a month, build OKfirst in a release 17 May 2004DEqMSa tool to perform statistical analysis of differential protein expression for quantitative proteomics data.901 distinct IPs a month, build OKfirst in a release 31 Oct 2018normrNormalization and difference calling in ChIP-seq data866 distinct IPs a month, build warningsfirst in a release 18 Oct 2016proDADifferential Abundance Analysis of Label-Free Mass Spectrometry Data864 distinct IPs a month, build OKfirst in a release 30 Oct 2019scDDMixture modeling of single-cell RNA-seq data to identify genes with differential distributions845 distinct IPs a month, build OKfirst in a release 25 Apr 2017TRONCOTRONCO, an R package for TRanslational ONCOlogy844 distinct IPs a month, build OKfirst in a release 17 Apr 2015tigreTranscription factor Inference through Gaussian process Reconstruction of Expression822 distinct IPs a month, build OKfirst in a release 23 Apr 2010CoGAPSCoordinated Gene Activity in Pattern Sets805 distinct IPs a month, build OKfirst in a release 18 Oct 2010NormalyzerDEEvaluation of normalization methods and calculation of differential expression analysis statistics797 distinct IPs a month, build OKfirst in a release 31 Oct 2018wavClusteRSensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data791 distinct IPs a month, build OKfirst in a release 14 Oct 2014phenopathGenomic trajectories with heterogeneous genetic and environmental backgrounds785 distinct IPs a month, build OKfirst in a release 31 Oct 2017baconControlling bias and inflation in association studies using the empirical null distribution783 distinct IPs a month, build OKfirst in a release 4 May 2016ASSIGNAdaptive Signature Selection and InteGratioN (ASSIGN)770 distinct IPs a month, build OKfirst in a release 14 Apr 2014metaseqR2An 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 2020EBcoexpressEBcoexpress for Differential Co-Expression Analysis729 distinct IPs a month, build warningsfirst in a release 2 Apr 2012R3CPET3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process727 distinct IPs a month, build warningsfirst in a release 17 Apr 2015sccompDifferential Composition and Variability Analysis for Single-Cell Data715 distinct IPs a month, build OKfirst in a release 27 Apr 2022AMARETTORegulatory 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 2019HiLDAConducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation695 distinct IPs a month, build OKfirst in a release 30 Oct 2019RJMCMCNucleosomesBayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)691 distinct IPs a month, build OKfirst in a release 25 Apr 2017BUScorrectBatch Effects Correction with Unknown Subtypes665 distinct IPs a month, build OKfirst in a release 31 Oct 2018PROPSPRObabilistic Pathway Score (PROPS)659 distinct IPs a month, build OKfirst in a release 31 Oct 2017BUMHMMComputational pipeline for computing probability of modification from structure probing experiment data654 distinct IPs a month, build OKfirst in a release 25 Apr 2017bandleAn R package for the Bayesian analysis of differential subcellular localisation experiments646 distinct IPs a month, build warningsfirst in a release 27 Apr 2022RIVERR package for RIVER (RNA-Informed Variant Effect on Regulation)639 distinct IPs a month, build OKfirst in a release 25 Apr 2017ctsGEClustering of Time Series Gene Expression data636 distinct IPs a month, build OKfirst in a release 18 Oct 2016BANDITSBANDITS: Bayesian ANalysis of DIfferenTial Splicing634 distinct IPs a month, build OKfirst in a release 3 May 2019DMCFBDifferentially Methylated Cytosines via a Bayesian Functional Approach626 distinct IPs a month, build OKfirst in a release 30 Oct 2019BaalChIPBaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes623 distinct IPs a month, build warningsfirst in a release 18 Oct 2016GmicRCombines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)620 distinct IPs a month, build warningsfirst in a release 30 Oct 2019protGearProtein Micro Array Data Management and Interactive Visualization603 distinct IPs a month, build OKfirst in a release 27 Apr 2022BUSseqBatch Effect Correction with Unknow Subtypes for scRNA-seq data600 distinct IPs a month, build OKfirst in a release 27 Oct 2021gemma.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 2022ternarynetTernary Network Estimation583 distinct IPs a month, build OKfirst in a release 2 Apr 2012IgGeneUsageDifferential gene usage in immune repertoires573 distinct IPs a month, build OKfirst in a release 30 Oct 2019scMETBayesian modelling of cell-to-cell DNA methylation heterogeneity564 distinct IPs a month, build errorfirst in a release 2 Nov 2022covEBEmpirical Bayes estimate of block diagonal covariance matrices560 distinct IPs a month, build OKfirst in a release 18 Oct 2016CBNplotplot bayesian network inferred from gene expression data based on enrichment analysis results559 distinct IPs a month, build OKfirst in a release 26 Apr 2023DifferentialRegulationDifferentially regulated genes from scRNA-seq data554 distinct IPs a month, build OKfirst in a release 27 Apr 2022hummingbirdBayesian Hidden Markov Model for the detection of differentially methylated regions546 distinct IPs a month, build OKfirst in a release 28 Oct 2020GWAS.BAYESBayesian analysis of Gaussian GWAS data546 distinct IPs a month, build OKfirst in a release 28 Oct 2020ClomialInfers clonal composition of a tumor542 distinct IPs a month, build OKfirst in a release 14 Apr 2014GRENITSGene Regulatory Network Inference Using Time Series531 distinct IPs a month, build OKfirst in a release 1 Nov 2011scDDboostA compositional model to assess expression changes from single-cell rna-seq data521 distinct IPs a month, build OKfirst in a release 2 Nov 2022graperAdaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes520 distinct IPs a month, build OKfirst in a release 3 May 2019BayesKnockdownBayesKnockdown: Posterior Probabilities for Edges from Knockdown Data515 distinct IPs a month, build OKfirst in a release 18 Oct 2016roastgsaRotation based gene set analysis509 distinct IPs a month, build OKfirst in a release 25 Oct 2023BAGSA Bayesian Approach for Geneset Selection507 distinct IPs a month, build errorfirst in a release 15 Oct 2013omicplotRVisual Exploration of Omic Datasets Using a Shiny App504 distinct IPs a month, build OKfirst in a release 1 May 2018ccfindRCancer Clone Finder502 distinct IPs a month, build OKfirst in a release 1 May 2018retrofitRETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics498 distinct IPs a month, build OKfirst in a release 26 Apr 2023geminiGEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens496 distinct IPs a month, build OKfirst in a release 30 Oct 2019IsoBayesIsoBayes: Single Isoform protein inference Method via Bayesian Analyses491 distinct IPs a month, build OKfirst in a release 25 Oct 2023ClustIRRClustering of Immune Receptor Repertoires484 distinct IPs a month, build errorfirst in a release 25 Oct 2023limpaQuantification and Differential Analysis of Proteomics Data484 distinct IPs a month, build OKfirst in a release 16 Apr 2025BASiCStanStan implementation of BASiCS478 distinct IPs a month, build warningsfirst in a release 2 Nov 2022BPRMethModel higher-order methylation profiles464 distinct IPs a month, build errorfirst in a release 18 Oct 2016banoccBayesian ANalysis Of Compositional Covariance452 distinct IPs a month, build OKfirst in a release 25 Apr 2017cellmigUncertainty-aware quantitative analysis of high-throughput live cell migration data444 distinct IPs a month, build errorfirst in a release 30 Oct 2025MetaboDynamicsBayesian analysis of longitudinal metabolomics data442 distinct IPs a month, build OKfirst in a release 16 Apr 2025INTACTIntegrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis442 distinct IPs a month, build OKfirst in a release 26 Apr 2023beerBayesian Enrichment Estimation in R424 distinct IPs a month, build errorfirst in a release 27 Apr 2022BG2Performs Bayesian GWAS analysis for non-Gaussian data using BG2418 distinct IPs a month, build OKfirst in a release 26 Apr 2023OpenStatsA Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association412 distinct IPs a month, build OKfirst in a release 28 Apr 2020calmCovariate Assisted Large-scale Multiple testing398 distinct IPs a month, build OKfirst in a release 30 Oct 2019plasmutStratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic378 distinct IPs a month, build OKfirst in a release 25 Oct 2023mfaBayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations376 distinct IPs a month, build errorfirst in a release 31 Oct 2017KBoostInference of gene regulatory networks from gene expression data375 distinct IPs a month, build OKfirst in a release 20 May 2021SanityRR/Bioconductor interface to the Sanity model gene expression analysis375 distinct IPs a month, build OKfirst in a release 30 Oct 2025MelissaBayesian clustering and imputationa of single cell methylomes373 distinct IPs a month, built, not publishedfirst in a release 3 May 2019DOTSeqGenome-wide Detection of Differential ORF Usage371 distinct IPs a month, build OKfirst in a release 29 Apr 2026HiCPottsHiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C365 distinct IPs a month, build OKfirst in a release 30 Oct 2025StatescopeRStatescopeR framework for discovery of cell states from cell type-specific gene expression profiles inferred from bulk mRNA profiles364 distinct IPs a month, build errorfirst in a release 29 Apr 2026CBN2PathCBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunctive Bayesian Networks321 distinct IPs a month, build OKfirst in a release 30 Oct 2025queeemsQuantify the Extent of Evolutionary Evidence in Molecular Sequences275 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 2026
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