README.md

In jinzhuangdou/DCCA: Tools for single cell multi-omics analysis \

DCCA

DCCA is an R package for single cell multi-omic integration analysis, developed and maintained by Ken chen's lab in MDACC. It performs CCA on cell and feature levels simulaneously to integrate two single cell profiles.

Check out our paper (xx) for a more complete description of the methods and analyses.

Once two datasets are integrated, the package also provides functionality for further data exploration, analysis, and visualization. Users can:

• Jointly Defining Cell Types from scRNA-seq and scATAC-seq
• B
• C

Instructions, documentation, and tutorials can be found at:

• https://

Improvements and new features will be added on a regular basis, please contact [e-mail] with any question.

Version History

June 28, 2020

• Version 0.0 released (initail release)

System Requirements

Hardware requirements

The DCCA package requires only a standard computer with enough RAM to support the in-memory operations. For minimal performance, please make sure that the computer has at least about 2 GB of RAM. For optimal performance, we recommend a computer with the following specs:

• RAM: 16+ GB
• CPU: 4+ cores, 2.3 GHz/core

Before setting up the DCCA package, users should have R version 3.6.0 or higher, and several packages set up from CRAN and other repositories. The user can check the dependencies in DESCRIPTION.

Installation

DCCA is written in R and can be installed by following R commands:

install.packages('devtools')
library(devtools)
install_github('xx/DCCA')

Usage

For usage examples and guided walkthroughs, check the vignettes directory of the repo.

• Integrating Multiple Single-Cell RNA-seq Datasets

• Jointly Defining Cell Types from scRNA-seq and scATAC-seq

Sample Datasets

The DCCA package provides a small simulated dataset for basic demos of the functions, you can find it in folder liger/inst/test1/small.data.RDS.

We also provide a set of scRNA-seq and scATAC-seq datasets for real-world style demos. These datasets are as follows:

• scATAC and scRNA data provided by 10X Genomics, access the pre-processed data from here. The data sources are:
  • pbmc.atac.expression.mat.RDS: raw data can be accessed here, created by Cell Ranger ATAC 1.1.0;
  • pbmc.rna.expression.mat.RDS: raw data can be accessed here, created by Cell Ranger 3.0.0.

Corresponding tutorials can be found in section Usage above.

License

This project is covered under the GNU General Public License 3.0.

jinzhuangdou/DCCA documentation built on June 29, 2020, 12:54 a.m.