ArticleBioinformatics (Oxford, England)2018
chromswitch: a flexible method to detect chromatin state switches.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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
7 citing papers in PubMed.
- Robust chromatin state annotation.Genome research · 2024Article
- A framework for group-wise summarization and comparison of chromatin state annotations.Bioinformatics (Oxford, England) · 2023Article
- Computational methods to explore chromatin state dynamics.Briefings in bioinformatics · 2022Review
- Fast detection of differential chromatin domains with SCIDDO.Bioinformatics (Oxford, England) · 2021Article
- Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in Cancer.Frontiers in genetics · 2021Article
- A comprehensive resource for retrieving, visualizing, and integrating functional genomics data.Life science alliance · 2020Article
- Automatic detection of genomic regions with informative epigenetic patterns.BMC genomics · 2018Article
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Authors and funding
2 authors.
Funding
Abstract
Summary: Chromatin state plays a major role in controlling gene expression, and comparative analysis of ChIP-seq data is key to understanding epigenetic regulation. We present chromswitch, an R/Bioconductor package to integrate epigenomic data in a defined window of interest to detect an overall switch in chromatin state. Chromswitch accurately classifies a benchmarking dataset, and when applied genome-wide, the tool successfully detects chromatin changes that result in brain-specific expression. Availability and implementation: Chromswitch is implemented as an R package available from Bioconductor at https://bioconductor.org/packages/chromswitch. All data and code for reproducing the analysis presented in this paper are available at https://doi.org/10.5281/zenodo.1101260. Supplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
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