R Observatory: Metrics for OpEnCAST version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

OpEnCAST

0.1.1Package record

Optimized Ensemble Model for C and A Methylation Search in Plant

0packages depend

3.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Abhik SarkarCRAN page ↗

DNA methylation is an important epigenetic process that regulates gene activity through chemical modifications of DNA without changing its sequence. 'OpEnCAST' is a plant-specific ensemble-based prediction package that identifies 4mC, 5mC and 6mA methylation sites directly from DNA sequences. It combines multiple machine learning algorithms trained on monocot (Oryza sp.) and dicot (Arabidopsis sp.) reference models to deliver accurate predictions. This methodology is being inspired by the ensemble algorithm for methylation prediction developed by Wang et al. (2022) doi:10.1186/s12859-022-04756-1.

Install

R (CRAN)Ubuntu (r2u)

install.packages("OpEnCAST", 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-opencast

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

13OK

Additional issues

donttest

CRAN check page ↗

Slowest check: 2.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 2
Examples that run: 0%2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 100%

How these are measured

Downloads

3.8K

CRAN downloads in the past year

Rank #15,598 · ~10/day · ~314/mo

Releases R versions

Daily download trend is not available in this view yet.

28830 days

77990 days

3.8K1 year

Compare downloads with other packages →

Also on52 r2u

How downloads are counted

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing OpEnCAST adds 21 packages (13 with compiled code, 30 MB of source tarballs). Heaviest: stringi 11 MB, sp 4.3 MB, seqinr 3.4 MB. 1 more not on CRAN is not measured.

Depends (0)

none

Imports (7)

Biostrings seqinr stringr tibble entropy ftrCOOLstats

LinkingTo (0)

none

Suggests (5)

caret kernlab ranger xgboost gbm

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (6)

Abhik Sarkar

Author, Maintainer since 0.1.1 (2026)

Sunil Archak

Author

Dwijesh Chandra Mishra

Author

Sneha Murmu

Author

Dipro Sinha

Author

Md Yeasin

Author

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.1.1Latest
record
2026-01-08 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-01-08
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Download size: 8.6 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("OpEnCAST")

Format

Sarkar, A., Archak, S., Mishra, D. C., Murmu, S., Sinha, D., & Yeasin, M. (2026). OpEnCAST: Optimized Ensemble Model for C and A Methylation Search in Plant (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.OpEnCAST

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for OpEnCAST version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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