Bioconductor Packages

A babysitter's package for reproducible RNA-seq analysis

A step-by-step guide to analyzing CAGE data using R/Bioconductor

Easy and efficient ensemble gene set testing with EGSEA

Package for the Comprehensive Analysis of Transcriptomic Data

Gene Expression Normalization Workflow

GeoMx Digital Spatial Profiler (DSP) data analysis workflows

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

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

Gene-level RNA-seq differential expression and pathway analysis using Rsubread and the edgeR quasi-likelihood pipeline

TCGA Workflow Analyze cancer genomics and epigenomics data using Bioconductor packages

Genomic Annotation Resources

Using Bioconductor for Microarray Analysis

A Bioconductor Workflow to Detect Differential Binding in ChIP-seq Data

csaw User's Guide

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

A plyranges and tximeta workflow

Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching

Using Bioconductor with High Throughput Assays

Changing genomic coordinate systems with rtracklayer::liftOver

An end to end workflow for differential gene expression using Affymetrix microarrays

A cross-package Bioconductor workflow for analysing methylation array data

recount workflow: accessing over 70,000 human RNA-seq samples with Bioconductor

RNA-seq workflow for differential transcript usage following Salmon quantification

RNA-seq workflow: gene-level exploratory analysis and differential expression

Seqpac: A Framework for smallRNA analysis in R using Sequence-Based Counts

Introduction to Bioconductor for Sequence Data

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

Annotating Genomic Variants