BioM2

1.1.3

Biologically Explainable Machine Learning Framework

0packages depend

3.5Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Shunjie ZhangFirst published 2023-09-2115 releasesCRAN page ↗

Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) doi:10.48550/arXiv.1712.00336.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) doi:10.2202/1544-6115.1128 and Langfelder and Horvath (2008) doi:10.1186/1471-2105-9-559 ) methods.

Install

R (CRAN)Ubuntu (r2u)

install.packages("BioM2", repos = "https://cloud.r-project.org/")

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

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-biom2

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

Health

CRAN checks

1NOTE12OK

Failing flavors

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

Slowest check: 5.9 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 3 earlier snapshots

OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 668 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.5K

CRAN downloads in the past year

Rank #11,912 · ~10/day · ~293/mo

Releases R versions

Daily download trend is not available in this view yet.

25630 days

85090 days

3.5K1 year

Compare downloads with other packages →

Also on482 r2u

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (20)

WGCNA mlr3 CMplot ggsci ROCR caret ggplot2 ggpubr viridis ggthemes ggstatsplot htmlwidgets mlr3verseparalleluwot webshot wordcloud2 ggforce igraph ggnetwork

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Shunjie Zhang

Author, Maintainer

Authors (2)

Shunjie Zhang

Author, Maintainer

Junfang Chen

Author · added in 1.0.1

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.3Latest
2025-07-17 · current release · diff ↗
1.1.2
2025-05-14 · diff ↗
unarchivedReturned to CRAN
2025-05-14
archivedRemoved from CRAN
2025-05-01
requires orphaned package 'jiebaR'
R
R 4.5.0 released · 2025-04-11
1.1.1
2025-02-19 · diff ↗
1.1.0
2024-09-20 · diff ↗
1.0.10
2024-08-20 · diff ↗
1.0.9
2024-08-01 · diff ↗
1.0.8
2024-07-18 · diff ↗
1.0.7
2024-06-09 · diff ↗
1.0.6
2024-05-16 · diff ↗
unarchivedReturned to CRAN
2024-05-16
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-04-20
issues were not corrected in time

Show 7 earlier events

1.0.5
2024-03-10 · diff ↗
1.0.4
2024-02-29 · diff ↗
1.0.3
2024-01-11 · diff ↗
1.0.2
2023-10-25 · diff ↗
1.0.1
2023-09-27 · diff ↗
1.0
2023-09-21
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-09-21
Total releases: 15 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 3.2 MB / 7 files
Download size: 3.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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