Comprehensive Reproducibility Framework for R and Bioinformatics Analysis R package Capsule version 0.2.0 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. Software Depends: R (>= 4.0.0) Imports: renv, jsonlite, digest, yaml, cli, utils Suggests: testthat (>= 3.0.0) Abu SAADAT <saadatabu1996@gmail.com> Comprehensive R Archive Network (CRAN) Abu SAADAT [aut, cre] (ORCID: <https://orcid.org/0000-0001-9636-2513>, affiliation: Università degli Studi della Campania Luigi Vanvitelli) MIT + file LICENSE (https://CRAN.R-project.org/package=Capsule/LICENSE) 2025-11-11 application/tgz https://CRAN.R-project.org/package=Capsule doi:10.32614/CRAN.package.Capsule