# Modeling for Single-Cell Open Chromatin Analysis

## Documentation for package ‘MOCHA’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.callOpenTiles_ArchR | 'callOpenTiles' Perform peak-calling on a set of fragments or an ArchR Project.
.counts_plot_default_theme | Default ggplot theme for counts plot
.gene_plot_theme | Common theme for gene plots
addAccessibilityShift | 'addAccessibilityShift'
addMotifSet | 'addMotifSet'
annotateTiles | 'annotateTiles'
callOpenTiles | 'callOpenTiles' Perform peak-calling on a set of fragments or an ArchR Project.
callOpenTiles-method | 'callOpenTiles' Perform peak-calling on a set of fragments or an ArchR Project.
differentialsToGRanges | 'differentialsToGRanges' Converts a data.frame matrix to a GRanges, preserving additional columns as GRanges metadata
exampleBlackList | exampleBlackList
exampleCellColData | exampleCellColData
exampleFragments | exampleFragments
extractRegion | 'extractRegion'
filterCoAccessibleLinks | 'filterCoAccessibleLinks'
finalModelObject | finalModelObject
getCellPopMatrix | 'getCellPopMatrix'
getCoAccessibleLinks | 'getCoAccessibleLinks'
getDifferentialAccessibleTiles | 'getDifferentialAccessibleTiles'
getPopFrags | Extract fragments by populations from an ArchR Project
getSampleTileMatrix | 'getSampleTileMatrix'
GRangesToString | 'GRangesToString' Converts a GRanges object to a string in the format 'chr1:100-200'
plotConsensus | 'plotConsensus'
plotRegion | 'plotRegion'
StringsToGRanges | 'StringsToGRanges'
subsetMOCHAObject | 'subsetObject'
youden_threshold | youden_threshold