MOCHA: Modeling for Single-Cell Open Chromatin Analysis

A statistical framework and analysis tool for open chromatin analysis designed specifically for single cell ATAC-seq (Assay for Transposase-Accessible Chromatin) data, after cell type/cluster identification. These novel modules remove unwanted technical variation, identify open chromatin, robustly models repeated measures in single cell data, implement advanced statistical frameworks to model zero-inflation for differential and co-accessibility analyses, and integrate with existing databases and modules for downstream analyses to reveal biological insights. MOCHA provides a statistical foundation for complex downstream analysis to help advance the potential of single cell ATAC-seq for applied studies. Methods for zero-inflated statistics are as described in: Ghazanfar, S., Lin, Y., Su, X. et al. (2020) <doi:10.1038/s41592-020-0885-x>. Pimentel, Ronald Silva, "Kendall's Tau and Spearman's Rho for Zero-Inflated Data" (2009) <https://scholarworks.wmich.edu/dissertations/721/>.

Package details

AuthorSamir Rachid Zaim [aut, ctb], Mark-Phillip Pebworth [aut, ctb], Imran McGrath [aut, cre], Lauren Okada [aut, ctb], Xiaojun Li [aut, ctb]
MaintainerImran McGrath <aifi.compbio.support@alleninstitute.org>
LicenseGPL (>= 3)
Version1.1.0
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("MOCHA")

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MOCHA documentation built on May 29, 2024, 2:25 a.m.