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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 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

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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=MAnorm2 to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.