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- W3100843338 abstract "Abstract Differential DNA methylation and chromatin accessibility are associated with disease development, particularly cancer. Methods that allow profiling of these epigenetic mechanisms in the same reaction and at the single-molecule or single-cell level continue to emerge. However, a challenge lies in jointly visualizing and analyzing the heterogeneous nature of the data and extracting regulatory insight. Here, we developed methylscaper, a visualization framework for simultaneous analysis of DNA methylation and chromatin landscapes. Methylscaper implements a weighted principle component analysis that orders sequencing reads, each providing a record of the chromatin state of one epiallele, and reveals patterns of nucleosome positioning, transcription factor occupancy, and DNA methylation. We demonstrate methylscaper’s utility on a long-read, single-molecule methyltransferase accessibility protocol for individual templates (MAPit) dataset and a single-cell nucleosome, methylation, and transcription sequencing (scNMT-seq) dataset. In comparison to other procedures, methylscaper is able to readily identify chromatin features that are biologically relevant to transcriptional status while scaling to larger datasets. Availability and implementation Methylscaper, is available on GitHub at https://github.com/rhondabacher/methylscaper . Contact rbacher@ufl.edu" @default.
- W3100843338 created "2020-11-23" @default.
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- W3100843338 date "2020-11-15" @default.
- W3100843338 modified "2023-09-23" @default.
- W3100843338 title "methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data" @default.
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- W3100843338 doi "https://doi.org/10.1101/2020.11.13.382465" @default.
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