External data sets to analyze with valr
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DESCRIPTION
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README.md
valrdata.Rproj

README.md

valrdata

Build Status

A Shiny app and R datapackage for demonstrating genome analysis with valr

Installation

# install.packages(devtools)
devtools::install_github("rnabioco/valrdata")

Shinyapp

valrdata::launch_valr_app()

Datasets

DNaseI Hypersensitivity Data

DNaseI Hypersensitivity sites in the human genome (hg19) identified by DNaseI-Seq in a set of 20 fetal tissues. Organized into a list of data_frames.

valrdata::dnase_data

Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195.

http://www.sciencemag.org/content/337/6099/1190.short

https://s3.amazonaws.com/bedtools-tutorials/web/maurano.dnaseI.tgz

Segway Encyclopedia

Annotations of human regulatory elements for 164 human cell types identified using Seqway organized in an extended bed+ wide format.

valrdata::segway_data

Libbrecht MW, Rodriguez O, Hoffman MM, Bilmes JA, Noble WS. 2016. A unified encyclopedia of human functional elements through fully automated annotation of 164 human cell types. Biorxiv preprint: http://dx.doi.org/10.1101/086025.

http://noble.gs.washington.edu/proj/encyclopedia/

http://noble.gs.washington.edu/proj/encyclopedia/segway_encyclopedia.bed.gz

Repetitive Elements

A dataset containing annotations for repeat classes in the hg19 human genome, as annotated by RepeatMasker in bed6+ format.

valrdata::repeat_data

http://genome.ucsc.edu/cgi-bin/hgTables

Gene Annotations

A dataset containing RefSeq refFlat gene annotations for hg19 in bed6 format.

valrdata::hg19_genes

http://genome.ucsc.edu/cgi-bin/hgTables