Bioconductor Packages

A babysitter's package for reproducible RNA-seq analysis

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

Genomic coordinates of CTCF binding sites, with orientation

Chimp and human brain data package

Helper files for CopywriteR

Easy and efficient ensemble gene set testing with EGSEA

EpipwR.data: Reference data for EpipwR

Package for the Comprehensive Analysis of Transcriptomic Data

Gene Expression Normalization Workflow

Illumina HumanMethylation data on sorted blood cell populations

Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells

Illumina 450k data on sorted cord blood cells

Illumina 450k/EPIC data on FACS and MACS umbilical blood cells

Illumina HumanMethylation data on sorted cord blood cell populations

Illumina HumanMethylation data on sorted frontal cortex cell populations

GeoMx Digital Spatial Profiler (DSP) data analysis workflows

LymphoSeq annotation databases

expression and copy number data on clear cell renal carcinoma 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

Annotation data for the TENET package

EBI/PSB cross-hybridisation study package

Affymetrix Data for Demonstration Purpose

exprSet for Alon et al. (1999) colon cancer data

Curated breast cancer gene expression data with survival and treatment information

Genomic coordinates of problematic genomic regions

Illumina DASL example microarray data

A plyranges and tximeta workflow

Leukemia's microarray gene expression data (expressionSet).

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

Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD).

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

Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010)