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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/>.
Reference manual: | MOCHA.pdf |
Vignettes: |
COVID-walkthrough Importing-From-Other-Sources |
Package source: | MOCHA_1.1.0.tar.gz |
Windows binaries: | r-devel: MOCHA_1.1.0.zip, r-release: MOCHA_1.1.0.zip, r-oldrel: MOCHA_1.1.0.zip |
macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): MOCHA_1.0.2.tgz, r-release (x86_64): MOCHA_1.0.2.tgz, r-oldrel (x86_64): MOCHA_1.0.2.tgz |
Old sources: | MOCHA archive |
Please use the canonical form https://CRAN.R-project.org/package=MOCHA to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.