exampleFragments

<p>Example input of ATAC fragments extracted from the PBMC_Small dataset
consisting of 2k cells and spanning chr1 and 2 (~2-300MB).
This subset consists of two cell populations: Clusters C2 and C5.
The data is publicly available with the ArchR package at
&lt;https://www.archrproject.com/reference/getTestProject.html&gt;</p>

datasets

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/>.

exampleFragments: exampleFragments

Description

Usage

Arguments

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