Capsule: Comprehensive Reproducibility Framework for R and Bioinformatics Analysis

A comprehensive reproducibility framework designed for R and bioinformatics workflows. Automatically captures the entire analysis environment including R session info, package versions, external tool versions ('Samtools', 'STAR', 'BWA', etc.), 'conda' environments, reference genomes, data provenance with smart checksumming for large files, parameter choices, random seeds, and hardware specifications. Generates executable scripts with 'Docker', 'Singularity', and 'renv' configurations. Integrates with workflow managers ('Nextflow', 'Snakemake', 'WDL', 'CWL') to ensure complete reproducibility of computational research workflows.

Version:	0.2.0
Depends:	R (≥ 4.0.0)
Imports:	renv, jsonlite, digest, yaml, cli, utils
Suggests:	testthat (≥ 3.0.0)
Published:	2025-11-11
DOI:	10.32614/CRAN.package.Capsule (may not be active yet)
Author:	Abu SAADAT [aut, cre] (affiliation: Università degli Studi della Campania Luigi Vanvitelli)
Maintainer:	Abu SAADAT <saadatabu1996 at gmail.com>
BugReports:	https://github.com/SAADAT-Abu/Capsule/issues
License:	MIT + file LICENSE
NeedsCompilation:	no
Materials:	README, NEWS
CRAN checks:	Capsule results

Documentation:

Reference manual:

Capsule.html , Capsule.pdf

Downloads:

Package source:	Capsule_0.2.0.tar.gz
Windows binaries:	r-devel: not available, r-release: Capsule_0.2.0.zip, r-oldrel: Capsule_0.2.0.zip
macOS binaries:	r-release (arm64): Capsule_0.2.0.tgz, r-oldrel (arm64): Capsule_0.2.0.tgz, r-release (x86_64): Capsule_0.2.0.tgz, r-oldrel (x86_64): Capsule_0.2.0.tgz

Linking:

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