A Shiny
app and R datapackage for demonstrating genome analysis with valr
# install.packages(devtools)
devtools::install_github("rnabioco/valrdata")
valrdata::launch_valr_app()
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
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
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
A dataset containing RefSeq refFlat
gene annotations for hg19
in bed6
format.
valrdata::hg19_genes
http://genome.ucsc.edu/cgi-bin/hgTables
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