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

FHCRC Genomics Shared Resource HuO22 Annotation Data (HuO22)

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)

A data package containing annotation data for JazaeriMetaData

LowMACAAnnotation

A set of annotation maps describing the Mouse Phenotype Ontology

FHCRC Genomics Shared Resource Mu15v1 Annotation Data (Mu15v1)

FHCRC Genomics Shared Resource Mu22v3 Annotation Data (Mu22v3)

Norway981 http://genome-www5.stanford.edu/ Annotation Data (Norway981)

FHCRC Nelson Lab OperonHumanV3 Annotation Data (OperonHumanV3)

Orthology mapping package

PartheenMetaData http://swegene.onk.lu.se Annotation Data (PartheenMetaData)

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

Roberts2005Annotation Annotation Data (Roberts2005Annotation)

SHDZ http://genome-www5.stanford.edu/ Annotation Data (SHDZ)

Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod)

Affymetrix Affymetrix AG Array annotation data (chip ag)

agcdf

Probe sequence data for microarrays of type ag

Using Bioconductor for Microarray Analysis

Affymetrix Affymetrix ATH1-121501 Array annotation data (chip ath1121501)

ath1121501cdf

Vectors used by frma for microarrays of type ath1121501

Probe sequence data for microarrays of type ath1121501

Affymetrix Affymetrix Celegans Array annotation data (chip celegans)

celeganscdf

Probe sequence data for microarrays of type celegans

Affymetrix Affymetrix DrosGenome1 Array annotation data (chip drosgenome1)

drosgenome1cdf

Probe sequence data for microarrays of type drosgenome1

Affymetrix Affymetrix Drosophila_2 Array annotation data (chip drosophila2)

drosophila2cdf