Bioconductor Packages

Analysis of Microbiome Differential Abundance by Pooling Tobit Models

An R package for subset-based association analysis of heterogeneous traits and subtypes

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

An R package for analysis of case-control studies in genetic epidemiology

Quantitative comparison of multiple ChIP-seq datasets

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

Analysis of single-cell epigenomics datasets with a Shiny App

Infers clonal composition of a tumor

Coordinated Gene Activity in Pattern Sets

An Investigation Across Different Species and Tissues

Methylation array and sequencing spatial analysis methods

Disease Ontology Semantic and Enrichment analysis

Genome-wide Detection of Differential ORF Usage

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Differential Binding Analysis of ChIP-Seq Peak Data

DiffLogo: A comparative visualisation of biooligomer motifs

Differentially regulated genes from scRNA-seq data

An R package for gene and isoform differential expression analysis of RNA-seq data

Ensemble of Gene Set Enrichment Analyses

Empirical RNA-seq Sample Size Analysis

Comparison, Benchmarking & QC of Epigenomic Datasets

find influential TF and Target based on multi-omics data

Gene Environment Wide Interaction Search Threshold

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

Visualise microarray and RNAseq data using gene ontology annotations

Find the most characteristic gene ontology terms for groups of human genes

Tools for manipulating GO and microarrays

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

Test and visualize gene overlaps

Automated analysis of high-throughput qPCR data

The removal of batch effects from datasets using a PCA and constrained optimisation based technique

Independent Hypothesis Weighting

Integrative Statistics of alleLe Dependent Expression

Interval-Wise Testing for Omics Data

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Estimation of the false discovery rate

Multiple Beta t-Tests

Single cell replicability analysis

A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Analysis of an ICA decomposition obtained on genomics data

Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

In-silico methods for genetic finemapping in inbred mice

Calculates Mulcom test

Testing multiple biological mediators simultaneously

Evaluation of normalization methods and calculation of differential expression analysis statistics

Operating characteristics plus sample size and local fdr for microarray experiments

An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

Optimal p-value weighting with independent information

OVESEG-test to detect tissue/cell-specific markers

Similarities of Ordered Gene Lists