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MOCHA
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]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-12-06
Latest Update:
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. Accessed 04 Jun. 2026.
Previous versions and publish date:
Other packages that cited MOCHA R package
View MOCHA citation profile
Other R packages that MOCHA depends,
imports, suggests or enhances
Complete documentation for MOCHA
Functions, R codes and Examples using
the MOCHA R package
Some associated functions: GRangesToString . StringsToGRanges . addAccessibilityShift . addMotifSet . annotateTiles . callOpenTiles-methods . differentialsToGRanges . dot-counts_plot_default_theme . dot-gene_plot_theme . exampleBlackList . exampleCellColData . exampleFragments . extractRegion . filterCoAccessibleLinks . finalModelObject . getCellPopMatrix . getCoAccessibleLinks . getDifferentialAccessibleTiles . getPopFrags . getSampleTileMatrix . plotConsensus . plotRegion . singlePopulationConsensusTiles . singlePopulationSampleTileMatrix . subsetMOCHAObject . youden_threshold .
Some associated R codes: addAccessibilityShift.R . addMotifSet.R . annotateTiles.R . calculate_intensities.R . callOpenTiles.R . callTilesBySample.R . co_accessibility.R . coverageFiles.R . determine_dynamic_range.R . dynamic_bins.R . estimate_differential_accessibility.R . extractRegion.R . filterCoAccessibleLinks.R . getCellPopMatrix.R . getCoAccessibleLinks.R . getDifferentialAccessibleTiles.R . getPopFrags.R . getSampleTileMatrix.R . make_prediction.R . models.R . plotConsensus.R . plotRegion.R . plottingUtils.R . singlePopulationConsensusTiles.R . singlePopulationSampleTileMatrix.R . subsetMOCHAObject.R . two_part.R . utils.R . zi_spearman.R . Full MOCHA package functions and examples
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