R: Comprehensive Reproducibility Framework for R and Bioinformatics Analysis

# Comprehensive Reproducibility Framework for R and Bioinformatics Analysis

## Documentation for package ‘Capsule’ version 0.2.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

capture_environment | Capture Environment State
capture_hardware | Capture Hardware Information
capture_session | Capture Complete Session Information
capture_system_libraries | Capture System Libraries
compare_snapshots | Compare Two Workflow Snapshots
create_renv_lockfile | Create renv Lockfile
create_repro_report | Create Reproducibility Report
export_for_cwl | Generate CWL (Common Workflow Language) Input
export_for_nextflow | Export Capsule Data for Nextflow
export_for_snakemake | Export Capsule Data for Snakemake
export_for_wdl | Create WDL (Workflow Description Language) Config
generate_docker | Generate Docker Configuration
generate_repro_script | Generate Reproducible Script
generate_singularity | Generate Singularity Definition File
get_conda_env_info | Get Conda Environment Info
get_data_lineage | Get Data Lineage
get_param_history | Get Parameter History
get_reference_info | Get Reference Genome Information
get_seed_history | Get Seed History
get_tool_versions | Get External Tool Versions
init_capsule | Initialize Capsule in Project
list_reference_sources | List Common Reference Genome Sources
list_snapshots | List Available Snapshots
restore_conda_env | Restore Conda Environment
restore_seed | Restore Random Seed
set_seed | Set and Track Random Seed
snapshot_packages | Track Package Versions and Dependencies
snapshot_workflow | Create Complete Workflow Snapshot
track_conda_env | Track Conda Environment
track_data | Track Data Provenance
track_external_tools | Track External Bioinformatics Tools
track_params | Track Analysis Parameters
track_reference_genome | Track Reference Genome
verify_data | Verify Data Integrity