MAnorm2: Tools for Normalizing and Comparing ChIP-seq Samples

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the premier technology for profiling genome-wide localization of chromatin-binding proteins, including transcription factors and histones with various modifications. This package provides a robust method for normalizing ChIP-seq signals across individual samples or groups of samples. It also designs a self-contained system of statistical models for calling differential ChIP-seq signals between two or more biological conditions as well as for calling hypervariable ChIP-seq signals across samples. Refer to Tu et al. (2021) <doi:10.1101/gr.262675.120> and Chen et al. (2021) <doi:10.1101/2021.07.27.453915> for associated statistical details.

Version: 1.2.0
Depends: R (≥ 3.5.0)
Imports: stats, graphics, methods, locfit (≥ 1.5.9), scales (≥ 0.3.0), statmod (≥ 1.4.34)
Suggests: gplots (≥ 3.0.1), DescTools (≥ 0.99.24), knitr, rmarkdown
Published: 2021-09-13
Author: Shiqi Tu ORCID iD [aut, cre]
Maintainer: Shiqi Tu <tushiqi at picb.ac.cn>
BugReports: https://github.com/tushiqi/MAnorm2/issues
License: GPL-3
URL: https://github.com/tushiqi/MAnorm2
NeedsCompilation: no
Citation: MAnorm2 citation info
Materials: README NEWS
CRAN checks: MAnorm2 results

Downloads:

Reference manual: MAnorm2.pdf
Vignettes: MAnorm2 for Normalizing and Comparing ChIP-seq Samples
Package source: MAnorm2_1.2.0.tar.gz
Windows binaries: r-devel: MAnorm2_1.2.0.zip, r-release: MAnorm2_1.2.0.zip, r-oldrel: MAnorm2_1.2.0.zip
macOS binaries: r-release (arm64): MAnorm2_1.2.0.tgz, r-release (x86_64): MAnorm2_1.2.0.tgz, r-oldrel: MAnorm2_1.2.0.tgz

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