BioMoR

0.1.1

Bioinformatics Modeling with Recursion and Autoencoder-Based Ensemble

0packages depend

2Kdownloads / year

52.8%test coverage

13/13checks pass

Overview

About

Maintained by MD. ArshadFirst published 2025-10-032 releasesCRAN page ↗

Tools for bioinformatics modeling using recursive transformer-inspired architectures, autoencoders, random forests, XGBoost, and stacked ensemble models. Includes utilities for cross-validation, calibration, benchmarking, and threshold optimization in predictive modeling workflows. The methodology builds on ensemble learning (Breiman 2001 doi:10.1023/A:1010933404324), gradient boosting (Chen and Guestrin 2016 doi:10.1145/2939672.2939785), autoencoders (Hinton and Salakhutdinov 2006 doi:10.1126/science.1127647), and recursive transformer efficiency approaches such as Mixture-of-Recursions (Bae et al. 2025 doi:10.48550/arXiv.2507.10524).

Install

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

install.packages("BioMoR", 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-biomor

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-BioMoR

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-BioMoR

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

Health

CRAN checks

13OK

Slowest check: 4.3 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.25

52.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: not tracked
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

CRAN downloads in the past year

Rank #19,933 · ~6/day · ~171/mo

Releases R versions

Daily download trend is not available in this view yet.

19330 days

60590 days

2K1 year

Compare downloads with other packages →

Also on2.2K r2u56 autocran

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (7)

caret recipes themis xgboost magrittr dplyr pROC

LinkingTo (0)

none

Suggests (9)

randomForest testthat PRROC ggplot2 purrr tibble yardstick knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 453 (51%)Rd 302 (34%)Vignettes 134 (15%)

Code characteristics

Cyclomatic complexity: 1.5 median / 3 max
Test cases: 5 / 0.25 per code line

Test coverage

Line coverage

53%

Expression

47.8%

Tests / Examples

52.8% / – ex

Functions

12 9 exported

Complexity

1.6 avg / 3 max

Call network

12 nodes / 4 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

12 functions

Function	Cyclo	Coverage
get_embeddings exp	1	0%
prepare_model_data exp	1	0%
train_autoencoder exp	1	0%
biomor_run_pipeline	2	0%
calibrate_model	3	0%
train_biomor	1	0%

People & History

People (1)

Maintainer (1)

MD. Arshad

Author, Maintainer

Authors (1)

MD. Arshad

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.1.1Latest
2025-12-11 · current release · diff ↗
0.1.0
2025-10-03
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-10-03
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.2.0
Download size: 17 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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