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 (source, R code) |
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:
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