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

Probe-level Expression Change Averaging

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

Transcriptome instability analysis

Genomic Annotation Resources

Analysis of SUrvival and RIsk prediction in patients based on gene signatures

A plyranges and tximeta workflow

Global Test for Counts

Linear Models for Microarray and Omics Data

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

Preprocessing tools for oligonucleotide arrays

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

L1-regularization based methods for detection of differential splicing

RNA-seq workflow for differential transcript usage following Salmon quantification

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

Rotation based gene set analysis

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

Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Supervised Normalization of Microarrays

Annotating Genomic Variants