MOCHA: Modeling for Single-Cell Open Chromatin Analysis

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/>.

Version:	1.1.0
Depends:	R (≥ 4.1.0)
Imports:	data.table, plyranges (≥ 1.14.0), dplyr, GenomicRanges, RaggedExperiment, MultiAssayExperiment, SummarizedExperiment, stringr, ggbio, wCorr, magrittr, rlang, AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, S4Vectors, assertthat, ensembldb, ggplot2, ggrepel, matrixStats, methods, qvalue, scales, tidyr, ggridges, pbapply, BSgenome, tidyselect, lifecycle
Suggests:	ArchR, RMariaDB, motifmatchr, BiocManager, TxDb.Hsapiens.UCSC.hg38.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19, withr, knitr, rmarkdown, chromVAR, testthat (≥ 3.0.0), uwot, irlba, glmmTMB, Matrix, waldo, purrr, lmerTest, Biobase, lme4, zip, rtracklayer, cowplot, mixtools, zoo
Published:	2024-01-25
Author:	Samir Rachid Zaim [aut, ctb], Mark-Phillip Pebworth [aut, ctb], Imran McGrath [aut, cre], Lauren Okada [aut, ctb], Xiaojun Li [aut, ctb]
Maintainer:	Imran McGrath <aifi.compbio.support at alleninstitute.org>
License:	GPL (≥ 3)
NeedsCompilation:	no
Additional_repositories:	https://imran-aifi.github.io/drat
Materials:	README NEWS
CRAN checks:	MOCHA results

Documentation:

Reference manual:	MOCHA.pdf
Vignettes:	COVID-walkthrough Importing-From-Other-Sources

Downloads:

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

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