ArticleBMC bioinformatics2011
Exploratory analysis of genomic segmentations with Segtools.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Segzoo: a turnkey system that summarizes genome annotations.Bioinformatics (Oxford, England) · 2026Article
- Effects of thymidylate synthase inhibitors differ in genomic uracilation and mutagenic potential.Life science alliance · 2026Article
- Robust chromatin state annotation.Genome research · 2024Article
- Assessing and assuring interoperability of a genomics file format.Bioinformatics (Oxford, England) · 2022Article
- Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns.PLoS computational biology · 2021Review
- Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments.eLife · 2020Article
- InTool Explorer: An Interactive Exploratory Analysis Tool for Versatile Visualizations of Neuroscientific Data.Frontiers in neuroanatomy · 2019Article
- Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid.Epigenetics & chromatin · 2017Article
- Integrative annotation of chromatin elements from ENCODE data.Nucleic acids research · 2013Article
- Unsupervised pattern discovery in human chromatin structure through genomic segmentation.Nature methods · 2012Article
- ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries.PloS one · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundAs genome-wide experiments and annotations become more prevalent, researchers increasingly require tools to help interpret data at this scale. Many functional genomics experiments involve partitioning the genome into labeled segments, such that segments sharing the same label exhibit one or more biochemical or functional traits. For example, a collection of ChlP-seq experiments yields a compendium of peaks, each labeled with one or more associated DNA-binding proteins. Similarly, manually or automatically generated annotations of functional genomic elements, including cis-regulatory modules and protein-coding or RNA genes, can also be summarized as genomic segmentations.
resultsWe present a software toolkit called Segtools that simplifies and automates the exploration of genomic segmentations. The software operates as a series of interacting tools, each of which provides one mode of summarization. These various tools can be pipelined and summarized in a single HTML page. We describe the Segtools toolkit and demonstrate its use in interpreting a collection of human histone modification data sets and Plasmodium falciparum local chromatin structure data sets.
conclusionsSegtools provides a convenient, powerful means of interpreting a genomic segmentation.
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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.