ArticleBioinformatics (Oxford, England)2023
excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Machine learning reveals sequence and genomic context features underlyingbioRxiv : the preprint server for biology · 2026Article
- Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project.PLoS genetics · 2026Article
- NetCIS: a network-based common insertion site pipeline for case-control Sleeping Beauty screens.Briefings in bioinformatics · 2026Article
- Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.Bioinformatics (Oxford, England) · 2026Article
- Egr1 is a sex-dependent regulator of neuronal chromatin, structural plasticity, and behaviour.Nature communications · 2025Article
- Mapping the Telomeric 3D Interactome with Telomere-C Reveals Repetitive Element Hubs Associated with Telomere Maintenance.bioRxiv : the preprint server for biology · 2025Article
- Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches.bioRxiv : the preprint server for biology · 2025Article
- The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate.Nature cell biology · 2025Article
- LINE1 elements at distal junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells.Genes & development · 2025Article
- Article
- Mechanisms of epigenomic and functional convergence between glucocorticoid- and IL4-driven macrophage programming.Nature communications · 2024Article
- Impact of genome build on RNA-seq interpretation and diagnostics.American journal of human genetics · 2024Article
- Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing.Nature communications · 2024Article
- Mechanisms of Epigenomic and Functional Convergence Between Glucocorticoid- and IL4-Driven Macrophage Programming.bioRxiv : the preprint server for biology · 2024Article
- Impact of genome build on RNA-seq interpretation and diagnostics.medRxiv : the preprint server for health sciences · 2024Article
- Article
- bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing.Bioinformatics (Oxford, England) · 2023Article
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Authors and funding
9 authors.
Funding
Abstract
summaryExclusion regions are sections of reference genomes with abnormal pileups of short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits are most pronounced in differential analysis settings. Several labs created exclusion region sets, available primarily through ENCODE and Github. However, the variety of exclusion sets creates uncertainty which sets to use. Furthermore, gap regions (e.g. centromeres, telomeres, short arms) create additional considerations in generating exclusion sets. We generated exclusion sets for the latest human T2T-CHM13 and mouse GRCm39 genomes and systematically assembled and annotated these and other sets in the excluderanges R/Bioconductor data package, also accessible via the BEDbase.org API. The package provides unified access to 82 GenomicRanges objects covering six organisms, multiple genome assemblies, and types of exclusion regions. For human hg38 genome assembly, we recommend hg38.Kundaje.GRCh38_unified_blacklist as the most well-curated and annotated, and sets generated by the Blacklist tool for other organisms. AVAILABILITY AND IMPLEMENTATION: https://bioconductor.org/packages/excluderanges/. Package website: https://dozmorovlab.github.io/excluderanges/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.