ArticleGenome biology2021
Bedshift: perturbation of genomic interval sets.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed.
- TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms.Nucleic acids research · 2024Article
- RgnTX: Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity.Computational and structural biotechnology journal · 2023Article
- Markov chains improve the significance computation of overlapping genome annotations.Bioinformatics (Oxford, England) · 2022Article
- GenomicDistributions: fast analysis of genomic intervals with Bioconductor.BMC genomics · 2022Article
- Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects.GigaScience · 2021Article
- Bedshift: perturbation of genomic interval sets.Genome biology · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Functional genomics experiments, like ChIP-Seq or ATAC-Seq, produce results that are summarized as a region set. There is no way to objectively evaluate the effectiveness of region set similarity metrics. We present Bedshift, a tool for perturbing BED files by randomly shifting, adding, and dropping regions from a reference file. The perturbed files can be used to benchmark similarity metrics, as well as for other applications. We highlight differences in behavior between metrics, such as that the Jaccard score is most sensitive to added or dropped regions, while coverage score is most sensitive to shifted regions.
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Registered trials
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.