Journal Article

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

Schep, Alicia N, Greenleaf, William J, Wu, Beijing, Buenrostro, Jason D

2017

Overview

ChromVar infers transcription-factor-associated accessibility from low-coverage or single-cell chromatin-accessibility data, thus enabling the clustering of cells and analysis of regulatory sequence motifs from sparse data sets. Single-cell ATAC-seq (scATAC) yields sparse data that make conventional analysis challenging. We developed chromVAR ( http://www.github.com/GreenleafLab/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 characterization of known and de novo sequence motifs associated with variation in chromatin accessibility.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 45 / 45/23 / 631/114/2114 / 631/114/2404 / 631/114/2785 / 631/114/794 / Accessibility / Algorithms / Animals / Annotations / B cells / Bias / Binding sites / Bioinformatics / Biological Microscopy / Biological Techniques / Biomedical Engineering/Biotechnology / brief-communication / Cell Line / Chromatin / Clustering / Data analysis / Data processing / DNA sequencing / Epigenomics - methods / Gene expression / Gene Expression Regulation / Genetic aspects / Leukemia / Life Sciences / Proteomics / Sequence Analysis, DNA - methods / Software / Stem cells / Transcription factors / Transcription Factors - metabolism