Biocview "Bayesian"

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

A Bayesian Approach for Geneset Selection

A collection of PCA methods

Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes

Adaptive Signature Selection and InteGratioN (ASSIGN)

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Analysis Of Differential Abundance Taking Sample Variation Into Account

Analysis Tools for scATACseq Data with CoGAPS

Analyze Gene Sets Collections Properites

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

An R package for the Bayesian analysis of differential subcellular localisation experiments

Approximate posterior estimation for GLM coefficients

a region-based method for quantitating the conservation and divergence of methylation patterns between species by high order features

A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association

Assess epigenetic heterogeneity with proportion of intermediate methylation

a statistical framework for differential pseudotime analysis in multiple single-cell RNA-seq samples

A tool for quantification of associations between genotypes and phenotypes in genome wide association studies (GWAS) with Bayesian inference and statistical learning

a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Batch Effects Correction with Unknown Subtypes

Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments

Bayesian ANalysis Of Compositional Covariance

Bayesian analysis of Gaussian GWAS data

Bayesian Analysis of Single-Cell Sequencing data

Bayesian clustering and imputationa of single cell methylomes

Bayesian Enrichment Estimation in R

Bayesian Hidden Markov Model for the detection of differentially methylated regions

Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations

Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

Bayesian hierarchical model for genome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)

Bayesian Inference of Regulatory Influence on Expression (biRte)

Bayesian mixture models for copy number polymorphisms

Bayesian modelling of cell-to-cell DNA methylation heterogeneity

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Better prediction by use of co-data: Adaptive group-regularized ridge regression

Cancer Clone Finder

Cell birth and death rates estimation

CEllular Latent Dirichlet Allocation

ChIP-Seq Statistical Power

Clustering of Time Series Gene Expression data

Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Computational pipeline for computing probability of modification from structure probing experiment data

Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

Controlling bias and inflation in association studies using the empirical null distribution

Coordinated Gene Activity in Pattern Sets

Covariate Assisted Large-scale Multiple testing

Decomposing Heterogeneous Cohorts using Omic Data Profiling

dgeAnalysis

Differential Abundance Analysis of Label-Free Mass Spectrometry Data

Differential gene expression analysis based on the negative binomial distribution

Differential gene usage in immune repertoires

Differentially Methylated Cytosines via a Bayesian Functional Approach

Differentially regulated genes from scRNA-seq data

dycone - analyze the dynamic landscape of metabolome data

EBcoexpress for Differential Co-Expression Analysis

EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices

Empirical Analysis of Digital Gene Expression Data in R

Empirical Bayes estimate of block diagonal covariance matrices

Estimating Local False Discovery Rates Using Empirical Bayes Methods

Estimating Local False Discovery Rates Using the Method of Moments

Evaluation of normalization methods and calculation of differential expression analysis statistics

GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens

Gene Regulatory Network Inference Using Time Series

Genome wide association studies of multiple traits with Bayesian multilvel models

Genomic trajectories with heterogeneous genetic and environmental backgrounds

genphen: tool for quantification of genotype-phenotype associations in genome wide association studies (GWAS)

GUI for limma Package with Affymetrix Microarrays

GUI for limma Package With Two Color Microarrays

Hierarchical Bayesian Analysis of Differential Expression and ALternative SPlicing (HBA-DEALS)

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Infer Copy Number Variation from Single-Cell RNA-Seq Data

Inference of gene regulatory networks from gene expression data

Infers clonal composition of a tumor

Integrative analysis of multi-omics data to infer regulatory networks

Interface to the RDP Classifier

Interpretable marker-based single-cell pseudotime using Bayesian parametric models

Linear Models for Microarray Data

Log Fold Change Distribution Tools for Working with Ratios of Counts

Meta-analysis for the metagenomic read counts data from different cohorts

Methylation Analysis Based on Signal Detection

MethylIT utility

Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

Model higher-order methylation profiles

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Multilevel Model for Multivariate Responses with Missing Values

Multi-Omics Factor Analysis (MOFA)

Multi-Omics Factor Analysis v2

Normalization and difference calling in ChIP-seq data

Pathway Enrichment Analysis Based on Bayesian Network

plot bayesian network inferred from gene expression data based on enrichment analysis results

PRObabilistic Pathway Score (PROPS)

Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Protein Micro Array Data Management and Interactive Visualization

R-Causal Library

Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data

Regression-based network inference using Bayesian Model Averaging

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data

R package for RIVER (RNA-Informed Variant Effect on Regulation)

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

Single Cell Differential Expression

Sparse Data Observations for Simulating Synthetic Abundance

Stan implementation of BASiCS

Ternary Network Estimation

Transcript expression inference and differential expression analysis for RNA-seq data

Transcriptional Rewiring

Transcription factor Inference through Gaussian process Reconstruction of Expression

TRONCO, an R package for TRanslational ONCOlogy

Variance Adaptive Shrinkage

Visual Exploration of Omic Datasets Using a Shiny App

Biocview "Bayesian"

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