MAnorm2

1.2.2

Tools for Normalizing and Comparing ChIP-seq Samples

0packages depend

3.5Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Shiqi TuFirst published 2021-09-133 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("MAnorm2", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("tushiqi/MAnorm2")

Development version from tushiqi/MAnorm2. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-manorm2

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-MAnorm2

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-MAnorm2

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 8.8 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,436 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 93%
Documented parameters: 77%
Return-value docs: 100%
References docs: 56%

Downloads

3.5K

CRAN downloads in the past year

Rank #13,446 · ~10/day · ~290/mo

Releases R versions

Daily download trend is not available in this view yet.

16330 days

75490 days

3.5K1 year

Compare downloads with other packages →

Also on177 r2u7 autocran

Repository

GitHub ↗ tushiqi/manorm2

33Stars

3Forks

6Open issues

0Open PRs

0Releases

50Commits

1Contributors

chip-seqdifferential-analysisempirical-bayesr-packagewinsorize-values

50 commits · Last activity 2022-11-03 · 0% stars, 30d

Stars over time

2025-05-14 · 312026-07-07 · 33

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/tushiqi/manorm2 on 2026-08-02.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (6)

statsgraphicsmethodslocfit scales (>= 0.3.0)statmod

LinkingTo (0)

none

Suggests (4)

gplots DescTools knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Shiqi Tu

Author, Maintainer

Authors (1)

Shiqi Tu

Author, Maintainer

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.2.2Latest
2022-10-28 · current release · diff ↗
1.2.1
2022-08-30 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.0
2021-09-13
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-09-13
Total releases: 3 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 761 KB / 1 file
Download size: 3.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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