rworkflows - Test, Document, Containerise, and Deploy R Packages

Reproducibility is essential to the progress of research, yet achieving it remains elusive even in computational fields. Continuous Integration (CI) platforms offer a powerful way to launch automated workflows to check and document code, but often require considerable time, effort, and technical expertise to setup. We therefore developed the rworkflows suite to make robust CI workflows easy and freely accessible to all R package developers. rworkflows consists of 1) a CRAN/Bioconductor-compatible R package template, 2) an R package to quickly implement a standardised workflow, and 3) a centrally maintained GitHub Action.

Last updated 2 months ago

softwareworkflowmanagementbioconductorcontainerscontinuous-integrationdockerdockerhubgithub-actionsreproducibilityworkflows

7.65 score 75 stars 6 scripts 333 downloads

EpiCompare - Comparison, Benchmarking & QC of Epigenomic Datasets

EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.

Last updated 26 days ago

epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsatacseqdnaseseqbenchmarkbenchmarkingbioconductorbioconductor-packagecomparisonhtmlinteractive-reporting

7.55 score 12 stars 47 scripts 76 downloads

orthogene - Interspecies gene mapping

`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.

Last updated 26 days ago

geneticscomparativegenomicspreprocessingphylogeneticstranscriptomicsgeneexpressionanimal-modelsbioconductorbioconductor-packagebioinformaticsbiomedicinecomparative-genomicsevolutionary-biologygenesgenomicsontologiestranslational-research

7.41 score 40 stars 1 packages 24 scripts 524 downloads

MungeSumstats - Standardise summary statistics from GWAS

The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.

Last updated 25 days ago

snpwholegenomegeneticscomparativegenomicsgenomewideassociationgenomicvariationpreprocessing

5.85 score 87 scripts 1.5k downloads