Comprehensive Reproducibility Framework for R and Bioinformatics Analysis
Capture Environment State
Capture Hardware Information
Capture Complete Session Information
Capture System Libraries
Compare Two Workflow Snapshots
Create renv Lockfile
Create Reproducibility Report
Build Dependency Graph
Calculate Checksum with Smart Algorithm Selection
Compare Package Lists
Compare Registry Files
Create Capsule config
Create example workflow script
Create .gitignore
Extract Package Information
Format R Value for Script
Format File Size
Generate Comparison Report
Generate docker-compose.yml
Generate Docker README
Generate Dockerfile
Generate .dockerignore
Get FASTA Statistics
Get Tool Path
Get Tool Version String
Load Conda Registry
Load Parameter Registry
Load Reference Registry
Load Provenance Registry
Load Seed Registry
Load Tools Registry
Parse Package Dependencies
Save Conda Registry
Save Parameter Registry
Save Reference Registry
Save Provenance Registry
Save Seed Registry
Save Tools Registry
Generate CWL (Common Workflow Language) Input
Export Capsule Data for Nextflow
Export Capsule Data for Snakemake
Create WDL (Workflow Description Language) Config
Generate Docker Configuration
Generate Reproducible Script
Generate Singularity Definition File
Get Conda Environment Info
Get Data Lineage
Get Parameter History
Get Reference Genome Information
Get Seed History
Get External Tool Versions
Initialize Capsule in Project
List Common Reference Genome Sources
List Available Snapshots
Restore Conda Environment
Restore Random Seed
Set and Track Random Seed
Track Package Versions and Dependencies
Create Complete Workflow Snapshot
Track Conda Environment
Track Data Provenance
Track External Bioinformatics Tools
Track Analysis Parameters
Track Reference Genome
Verify Data Integrity
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.