Bioconductor Packages

LRBaseDbs for AnnotationHub

MeSHDbs for AnnotationHub

Metabolites and proteins linked to PathBank pathways (for AnnotationHub)

Metabolites linked to WikiPathways pathways (for AnnotationHub)

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

A set of annotation maps describing the entire Disease Ontology

Easy and efficient ensemble gene set testing with EGSEA

Package for the Comprehensive Analysis of Transcriptomic Data

Gene Expression Normalization Workflow

A set of annotation maps describing the entire Gene Ontology

GeoMx Digital Spatial Profiler (DSP) data analysis workflows

A set of annotation maps describing the entire Human Disease Ontology

A set of annotation maps describing the entire Human Phenotype Ontology

Data package for JASPAR 2018

Data package for JASPAR database (version 2020)

Data package for JASPAR database (version 2022)

Data package for JASPAR database (version 2024)

LowMACAAnnotation

A set of annotation maps describing the Mouse Phenotype Ontology

Orthology mapping package

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

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

Genomic coordinates of problematic genomic regions

A plyranges and tximeta workflow

Input data for the geneplast package

Global Test for Counts

Unknown annotation data (chip hguDKFZ31)

Unknown annotation data (chip hgubeta7)

Anotation package for Hipathia package

A data package containing annotation data for humanCHRLOC

Linear Models for Microarray and Omics Data

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

Tools for conducting enrichment analysis of MeSH

Mapping of Metabolite IDs from Different Sources

A data package containing annotation data for mouseCHRLOC

Preprocessing tools for oligonucleotide arrays

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

Demonstration Data from rGenomeTracks Package

A data package containing annotation data for ratCHRLOC

A set of annotation maps for reactome

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

Pretrained models for scAnnotatR package