chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data

Single cell ATAC-seq (scATAC) yields sparse data that makes application of conventional analysis approaches challenging. We developed chromVAR, an R package for analyzing sparse chromatin accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation...

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Detalles Bibliográficos
Autores principales: Schep, Alicia N., Wu, Beijing, Buenrostro, Jason D., Greenleaf, William J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2017
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5623146/
https://www.ncbi.nlm.nih.gov/pubmed/28825706
http://dx.doi.org/10.1038/nmeth.4401
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author Schep, Alicia N.
Wu, Beijing
Buenrostro, Jason D.
Greenleaf, William J.
author_facet Schep, Alicia N.
Wu, Beijing
Buenrostro, Jason D.
Greenleaf, William J.
author_sort Schep, Alicia N.
collection PubMed
description Single cell ATAC-seq (scATAC) yields sparse data that makes application of conventional analysis approaches challenging. We developed chromVAR, an R package for analyzing sparse chromatin accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. chromVAR enables accurate clustering of scATAC-seq profiles and enables characterization of known and de novo sequence motifs associated with variation in chromatin accessibility.
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spelling pubmed-56231462018-02-21 chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data Schep, Alicia N. Wu, Beijing Buenrostro, Jason D. Greenleaf, William J. Nat Methods Article Single cell ATAC-seq (scATAC) yields sparse data that makes application of conventional analysis approaches challenging. We developed chromVAR, an R package for analyzing sparse chromatin accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. chromVAR enables accurate clustering of scATAC-seq profiles and enables characterization of known and de novo sequence motifs associated with variation in chromatin accessibility. 2017-08-21 2017-10 /pmc/articles/PMC5623146/ /pubmed/28825706 http://dx.doi.org/10.1038/nmeth.4401 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Schep, Alicia N.
Wu, Beijing
Buenrostro, Jason D.
Greenleaf, William J.
chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data
title chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data
title_full chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data
title_fullStr chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data
title_full_unstemmed chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data
title_short chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data
title_sort chromvar: inferring transcription factor-associated accessibility from single-cell epigenomic data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5623146/
https://www.ncbi.nlm.nih.gov/pubmed/28825706
http://dx.doi.org/10.1038/nmeth.4401
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