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. (2022) <doi:10.1186/s13059-022-02627-9> for associated statistical details.

Version:	1.2.2
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:	2022-10-28
DOI:	10.32614/CRAN.package.MAnorm2
Author:	Shiqi Tu [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

Documentation:

Reference manual:	MAnorm2.pdf
Vignettes:	MAnorm2 for Normalizing and Comparing ChIP-seq Samples

Downloads:

Package source:	MAnorm2_1.2.2.tar.gz
Windows binaries:	r-devel: MAnorm2_1.2.2.zip, r-release: MAnorm2_1.2.2.zip, r-oldrel: MAnorm2_1.2.2.zip
macOS binaries:	r-release (arm64): MAnorm2_1.2.2.tgz, r-oldrel (arm64): MAnorm2_1.2.2.tgz, r-release (x86_64): MAnorm2_1.2.2.tgz, r-oldrel (x86_64): MAnorm2_1.2.2.tgz
Old sources:	MAnorm2 archive

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