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: | 0.1.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | data.table, plyranges, dplyr, GenomicRanges, RaggedExperiment, MultiAssayExperiment, SummarizedExperiment, stringr, ggbio, wCorr, magrittr, rlang, AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, OrganismDbi, S4Vectors, assertthat, biovizBase, ensembldb, ggplot2, ggrepel, matrixStats, methods, qvalue, scales, tidyr, ggridges |
| Suggests: | ArchR, RMariaDB, motifmatchr, BiocManager, TxDb.Hsapiens.UCSC.hg38.refGene, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19, withr, knitr, rmarkdown, testthat (≥ 3.0.0) |
| Published: | 2022-12-06 |
| 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 <imran.mcgrath at alleninstitute.org> |
| License: | GPL (≥ 3) |
| NeedsCompilation: | no |
| Additional_repositories: | https://imran-aifi.github.io/drat |
| Materials: | README NEWS |
| CRAN checks: | MOCHA results |
| Reference manual: | MOCHA.pdf |
| Vignettes: |
COVID-walkthrough Comparing-Cell-Populations |
| Package source: | MOCHA_0.1.0.tar.gz |
| Windows binaries: | r-devel: MOCHA_0.1.0.zip, r-release: MOCHA_0.1.0.zip, r-oldrel: MOCHA_0.1.0.zip |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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