Bioconductor Packages

Data required for getting the gene set scores with NetActivity package

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

Supporting data for package OMICsPCA

Ob/ob Mice Data on Normal and High Fat Diet

FHCRC Nelson Lab OperonHumanV3 Annotation Data (OperonHumanV3)

Orthology mapping package

expression and copy number data on clear cell renal carcinoma samples

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

Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al.

Experimental data for the PathNet package

SELDI-TOF data of Breast cancer samples

Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells

Roberts2005Annotation Annotation Data (Roberts2005Annotation)

Supporting datasets for SBGNview package

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

A bioconductor package for sample quality check with next generation sequencing data

Integrating Multi-modal Single Cell Experiment datasets

Somatic Cancer Alterations

A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata

Data for the VariantTools tutorial

Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC).

Mappability tracks of Whole-genome Sequencing from the ENCODE Project

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

RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014

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

Data for testing of the package blima.

Gene expression dataset published by Schmidt et al. [2008] (MAINZ).

Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG).

Gene expression dataset published by Sotiriou et al. [2007] (UNT).

Gene expression dataset published by Miller et al. [2005] (UPP).

Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX).

Connectivity Map (version 2) Data

Affymetrix Affymetrix Celegans Array annotation data (chip celegans)

celeganscdf

Probe sequence data for microarrays of type celegans

cn.mops - Mixture of Poissons for CNV detection in NGS data

A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations

A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)

A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)

Curated breast cancer gene expression data with survival and treatment information

Curated Prostate Cancer Data

Curation of existing tuberculosis transcriptomic studies

Cancer Dependency Map Data Package