CeTF

An implementation of PCIT and RIF analysis in R

Overview

This package provides the necessary instructions for performing the Partial Correlation coefficient with Information Theory (PCIT) from Reverter and Chan 2008 and Regulatory Impact Factors (RIF) from Reverter et al. 2010 algorithm. The PCIT algorithm identifies meaningful correlations to define edges in a weighted network. The algorithm can be applied to any correlation-based network including but not limited to gene co-expression networks. While the RIF algorithm identify critical transcript factors (TF) from gene expression data. These two algorithms when combined provide a very relevant layer of information for gene expression studies (Microarray, RNA-seq and single-cell RNA-seq data).

Installation

To properly run ceTF package is necessary to install some dependencies. For Linux users is necessary to install the following dependencies:

• libcurl4-openssl-dev
• libxml2-dev
• libssl-dev
• gfortran
• build-essential
• libz-dev
• zlib1g-dev

To install R packages dependencies, run:

#CRAN dependencies
packagesCRAN <- c('BiocManager', 'crayon', 'dplyr', 'geomnet', 'GGally', 'ggplot2', 'ggpubr', 'ggrepel', 'kableExtra', 'knitr', 'network', 'pbapply', 'reshape2', 'rmarkdown', 'scales', 'testthat', 'tidyr')
install.packages(packagesCRAN[!packagesCRAN %in% installed.packages()[,1]])

#Bioconductor dependencies
packagesBioc <- c('airway', 'clusterProfiler', 'DESeq2', 'org.Hs.eg.db', 'SummarizedExperiment')
BiocManager::install(packagesBioc[!packagesBioc %in% installed.packages()[,1]])

Finally, to install ceTF package:

devtools::install_github("cbiagii/ceTF")

Docker

To install docker follow the instructions in the links below depending on your operating system

• CentOS: https://docs.docker.com/install/linux/docker-ce/centos/
• Debian: https://docs.docker.com/install/linux/docker-ce/debian/
• Fedora: https://docs.docker.com/install/linux/docker-ce/fedora/
• Ubuntu: https://docs.docker.com/install/linux/docker-ce/ubuntu/
• MacOS: https://docs.docker.com/docker-for-mac/install/
• Windows: https://docs.docker.com/docker-for-windows/install/

Docker pull

Once docker is installed, the next step is pull the ceTF image from dockerhub using the following command:

docker pull biagii/ceTF:0.99.0

Running image

There are several differents parameters to run the downloaded image. The most commom way is executing the following command:

docker run --rm -d -p PORT:PORT -e PASSWORD=password --name [ANY_NAME] -v /server/path/:/docker/path/ -e USERID=$UID biagii/ceTF:0.99.0

Once the docker image is running, the Rstudio interface with all the necessary dependencies will be made available, and of course the ceTF package, installed ready for use.

Help

Any questions contact the developer by email: biagi@usp.br