Capsule: Comprehensive Reproducibility Framework for R and Bioinformatics Analysis (original) (raw)
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 |
| Author: | Abu SAADAT  [aut, cre] (affiliation: Università degli Studi della Campania Luigi Vanvitelli) |
| Maintainer: | Abu SAADAT |
| BugReports: | https://github.com/SAADAT-Abu/Capsule/issues |
| License: | MIT + file |
| NeedsCompilation: | no |
| Materials: | README, NEWS |
| CRAN checks: | Capsule results |
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