MOCHA
CRANMOCHAMaRDI QIDQ86041FDOQ86041
Modeling for Single-Cell Open Chromatin Analysis
Lauren Okada, Imran McGrath, Mark-Phillip Pebworth, Samir Rachid Zaim, Xiaojun Li
Last update: 25 January 2024
Copyright license: GNU General Public License
Software version identifier: 0.1.0, 1.0.0, 1.0.1, 1.0.2, 1.1.0
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/>.
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