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MOCHA  

Modeling for Single-Cell Open Chromatin Analysis
View on CRAN: Click here


Download and install MOCHA package within the R console
Install from CRAN:
install.packages("MOCHA")

Install from Github:
library("remotes")
install_github("cran/MOCHA")

Install by package version:
library("remotes")
install_version("MOCHA", "1.1.0")



Attach the package and use:
library("MOCHA")
Maintained by
Imran McGrath
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-12-06
Latest Update: 2024-01-25
Description:
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) . Pimentel, Ronald Silva, "Kendall's Tau and Spearman's Rho for Zero-Inflated Data" (2009) .
How to cite:
Imran McGrath (2022). MOCHA: Modeling for Single-Cell Open Chromatin Analysis. R package version 1.1.0, https://cran.r-project.org/web/packages/MOCHA
Previous versions and publish date:
0.1.0 (2022-12-06 14:42), 1.0.0 (2023-06-12 14:30), 1.0.1 (2023-11-14 15:03), 1.0.2 (2023-12-21 12:40)
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