MAnorm2

1.2.2

Tools for Normalizing and Comparing ChIP-seq Samples

0packages depend

3.6Kdownloads / 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")

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

pak::pak("tushiqi/MAnorm2")

Development version from tushiqi/MAnorm2. Requires the pak package.

Release

# one-time r2u setup for Ubuntu (noble)

curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash

# then install

sudo apt install r-cran-manorm2

Fast Ubuntu binaries via r2u (no compilation). Run the setup once per machine.

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

sudo dnf copr enable iucar/cran

sudo dnf install R-CRAN-MAnorm2

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

sudo zypper install R-MAnorm2

RPMs auto-built from CRAN on openSUSE OBS.

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

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

Downloads

3.6K

CRAN downloads in the past year

Rank #12,777 · ~10/day · ~296/mo

MAnorm2 Releases R versions

Daily download trend is not available in this view yet.

36630 days

83590 days

3.6K1 year

Compare downloads with other packages →

Also on168 r2u26 autocran

Source & community

GitHub ↗

Repository stars, issues, and contributor activity are not tracked yet.

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

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

R 7,518 (51%)Rd 6,206 (42%)Vignettes 894 (6%)Other 86 (1%)

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

55 41 exported

Complexity

9.2 avg / 33 max

Call network

55 nodes / 40 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Shiqi Tu

Author, Maintainer

Authors (1)

Shiqi Tu

Author, Maintainer

Release 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
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet