Other packages > Find by keyword >

MOCHA  

Modeling for Single-Cell Open Chromatin Analysis
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]
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 15 Jul. 2026.
Previous versions and publish date:
0.1.0 (2022-12-06 14:42), 1.0.0 (2023-06-12 14:30), 1.0.1 (2023-11-14 15:03), 1.0.2 (2023-12-21 12:40), 1.1.0 (2024-01-25 13:20), (2026-07-09 08:09)
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

gscaLCA  
Generalized Structure Component Analysis- Latent Class Analysis & Latent Class Regression
Execute Latent Class Analysis (LCA) and Latent Class Regression (LCR) by using Generalized Structu ...
Download / Learn more Package Citations See dependency  
pulseTD  
Identification of Transcriptional Dynamics using Pulse Models via 4su-Seq Data and RNA-Seq Data
A tool for analyzing the transcription, processing and degradation rates of genes by 4sU-seq (the Me ...
Download / Learn more Package Citations See dependency  
SECFISH  
Disaggregate Variable Costs
These functions were developed within SECFISH project (Strengthening regional cooperation in the are ...
Download / Learn more Package Citations See dependency  
footBayes  
Fitting Bayesian and MLE Football Models
This is the first package allowing for the estimation, visualization and prediction of the most wel ...
Download / Learn more Package Citations See dependency  
gamlss.add  
Extra Additive Terms for Generalized Additive Models for Location Scale and Shape
Interface for extra smooth functions including tensor products, neural networks and decision trees. ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  

27,806

R Packages

239,283

Dependencies

73,837

Author Associations

27,807

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA