Bioconductor Packages

Inference of differential exon usage in RNA-Seq

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

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

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

Data Mining for RNA-seq data: normalization, feature selection and classification

DegNorm: degradation normalization for RNA-seq data

Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Utilities for Handling Single-Cell Droplet Data

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

Exploratory Data Analysis and Normalization for RNA-Seq

Ensemble of Gene Set Enrichment Analyses

Quality control and analysis tools for Illumina DNA methylation BeadChip

Empirical RNA-seq Sample Size Analysis

Publication-ready volcano plots with enhanced colouring and labeling

Seamless navigation through combined results of set-based and network-based enrichment analysis

Epigenetic Dissection of Intra-Sample-Heterogeneity

An effective identification of alternative splicing events using junction arrays and RNA-Seq data

ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition

Prediction of gestational age with Illumina HumanMethylation450 data

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Binomial test for Hi-C data analysis

Visualise microarray and RNAseq data using gene ontology annotations

Calculate growth-rate inhibition (GR) metrics

Reproducible GSEA Benchmarking

GUIDE-seq and PEtag-seq analysis pipeline

Projection-based Gating Strategy Optimization for Flow and Mass Cytometry

Tools for spliced gene structure manipulation and analysis

Representation and manipulation of short genomic alignments

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

HDF5 datasets as array-like objects in R

Filter replicated high-throughput transcriptome sequencing data

Independent Hypothesis Weighting

Integrative analysis of Multi-omics data for Alternative Splicing

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package

Automated Optimization of XCMS Data Processing parameters

Integrative Statistics of alleLe Dependent Expression

Identification of genetic Variants affecting Alternative Splicing

Methods for BCR single-cell embedding

Differential gene usage in immune repertoires

Intron-Exon Retention Estimator

Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments

Graphical User Interface for IsoCorrectoR

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

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis

Linear model and normality based normalization and transformation method (Linnorm)

LoomExperiment container

Monte Carlo Reference-based Consensus Clustering