R/z_data.R

In benja0x40/Tightrope: ChIP-seq normalization according to background reads density

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#' H3K27me3 ChIP-seq in mouse Neuronal Stem Cell (NSCs)
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#' @description
#'
#' COUNTS: Precomputed read count matrixes (mm10)
#'
#' METADATA: Annotation of experimental conditions
#'
#' SPIKEIN: Number of Drosophila reads (spike-in)
#'
#' @details
#' This ChIP-seq dataset was generated by reproducing experiments presented
#' in our study about the role of the H3.3K27M histone mutation in DIPG
#' (Mohammad et al., 2017), but adding spike-in with Drosophila chromatin
#' in the ChIP-seq protocol.
#' Briefly, H3K27me3 ChIP-seq experiments were performed in mouse NSCs, in
#' presence or absence of expression of the H3.3K27M histone mutant (K27M)
#' as well as with or without treatment with EPZ6438 (EPZ), an inhibitor of the
#' catalytic reaction producing the H3K27me3 histone mark.
#'
#' @references
#' Mohammad F., Weissmann S., Leblanc B., Pandey D.P. et al.
#' EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas.
#' Nature Medicine 2017 \url{http://dx.doi.org/10.1038/nm.4293}
"NSC_K27M"

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#' Ensembl genes - Homo sapiens - GRCh38 / hg38 (rel. 91, Dec. 2017)
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#' @keywords internal
"EGA91_human"

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#' Ensembl genes - Mus musculus - GRCm38 / mm10 (rel. 91, Dec. 2017)
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#' @keywords internal
"EGA91_mouse"

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#' UCSC CGIs - Homo sapiens - GRCh38 / hg38
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#' @keywords internal
"CGI_hg38"

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#' UCSC CGIs - Mus musculus - GRCm38 / mm10
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#' @keywords internal
"CGI_mm10"

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#' ENCODE blacklist - Homo sapiens - GRCh38 / hg38
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#' @keywords internal
"hg38_blacklist"

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#' ENCODE blacklist - Mus musculus - GRCm38 / mm10
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#' @keywords internal
"mm10_blacklist"