excluderanges

excluderanges removes reads overlapping curated exclusion regions from genome assemblies to improve biological signal in differential genomic analyses.

Key Features:

• R/Bioconductor package: Provided as an R/Bioconductor package for programmatic use with Bioconductor data structures.
• Targeted artifact regions: Addresses abnormal pileups of short sequencing reads by defining exclusion regions such as centromeres, telomeres, and short arms.
• Organism coverage: Includes comprehensive exclusion-region data for six different organisms.
• GenomicRanges objects: Supplies 82 GenomicRanges objects that standardize access to curated exclusion sets.
• Source integration: Exclusion sets assembled from multiple sources including ENCODE and GitHub.
• BEDbase API integration: Integrates with the BEDbase.org API for programmatic access to exclusion-region data.
• Recommended human blacklist: Recommends the hg38.Kundaje.GRCh38_unified_blacklist as a curated and annotated exclusion set for human assemblies.
• Blacklist tool sets: Suggests using sets generated by the Blacklist tool for non-human organisms.

Scientific Applications:

• Differential genomic analysis: Improves detection of true differential signals by excluding artifact-prone regions.
• Gene expression and epigenetics: Reduces false-positive signals in gene expression and epigenetic modification studies caused by anomalous read pileups.
• Exclusion-region assembly and annotation: Supports assembling and annotating exclusion-region sets across multiple genome assemblies.

Methodology:

Removes reads overlapping defined exclusion regions, provides 82 curated GenomicRanges objects assembled from sources including ENCODE and GitHub, integrates with the BEDbase.org API, and recommends hg38.Kundaje.GRCh38_unified_blacklist for human and Blacklist tool-generated sets for other organisms.