R-universe - saadat-abu (Abu Saadat)

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.

Last updated

4.25 score 8 stars 22 scripts 238 downloads

GIMP - Genomic Imprinting Methylation Patterns

A package for analyzing Imprinting Control Regions (ICRs) DNA methylation. Supports both processed methylation data and raw IDAT files from Illumina arrays. Provides specialized tools for imprinting analysis including defect detection and interactive visualizations.

Last updated

dnamethylationmicroarraypreprocessingqualitycontroldifferentialmethylationepigeneticsmethylationarraybioinformaticsmethylation-arraysshiny-app

2.60 score 2 stars 10 scripts