intePareto: Integrative Analysis of RNA-Seq and ChIP-Seq Data

Integrative analysis of gene expression (RNA-Seq data), and histone modification data for user-defined sets of histone marks (ChIP-Seq data) to discover consistent changes in genes between biological conditions. Additionally, Pareto optimization is used to prioritize genes based on the level of consistent changes in both RNA-Seq and ChIP-Seq data. Method is described in Cao, Y. et al. (2020) <doi:10.1186/s12864-020-07205-6>.

Version: 0.1.2
Depends: R (≥ 3.6.0)
Imports: GenomicRanges, GenomeInfoDb, IRanges, GenomicAlignments, biomaRt, Rsamtools, rPref, DESeq2
Suggests: knitr, rmarkdown
Published: 2021-06-18
Author: Yingying Cao [aut, cre]
Maintainer: Yingying Cao <yingying.cao at uni-due.de>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
Materials: README
CRAN checks: intePareto results

Documentation:

Reference manual: intePareto.pdf
Vignettes: intePareto

Downloads:

Package source: intePareto_0.1.2.tar.gz
Windows binaries: r-devel: intePareto_0.1.2.zip, r-release: intePareto_0.1.2.zip, r-oldrel: intePareto_0.1.2.zip
macOS binaries: r-release (arm64): intePareto_0.1.2.tgz, r-release (x86_64): intePareto_0.1.2.tgz, r-oldrel: intePareto_0.1.2.tgz
Old sources: intePareto archive

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