ConSReg 1.0.6

condition-specific regulation

# ConSReg [](https://opensource.org/licenses/MIT) Condition-specific regulations

# Getting Started ## 1. Installation ### 1.1 Python installation ConSReg can be installed using pip: `shell pip install --user ConSReg ` ### 1.2 R installation ConSReg requires several R packages: ChIPseeker, CoReg, gglasso and RRF.

To install ChIPSeeker from bioconductor, type the following commands in R environment: `R source("https://bioconductor.org/biocLite.R") biocLite("ChIPseeker") ` Please refer to the instructions described [here](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) for more details.

To install CoReg pakcage from GitHub, type the following commands in R environment: `R install.packages("devtools") library(devtools) install_github("LiLabAtVT/CoReg") ` Please refer to the GitHub page of CoReg project for more details: [link](https://github.com/LiLabAtVT/CoReg)

To install gglasso package from CRAN, type the following commands in R environment: `R install.pacakges("gglasso") ` Please refer to the link [here](https://cran.r-project.org/web/packages/gglasso/index.html) for more details.

To install RRF package from CRAN, type the following commands in R environment: `R install.pacakges("RRF") ` Please refer to the link [here](https://cran.r-project.org/web/packages/RRF/index.html) for more details.

## 2. Sample datasets Sample datasets can be found in data folder.

## 3. Analysis We provide code for analyzing the sample datasets in two jupyter notebooks located in the root folder of this project: bulk_analysis.ipynb (for bulk RNA-seq data) and single_cell_analysis.ipynb (for single cell RNA-seq data).

## 4. Publication ConSReg is currently in review at Genome Research. We will soon provide a pre-print version of our manuscript.

Qi Song, Jiyoung Lee, Shamima Akter, Ruth Grene, Song Li. Accurate prediction of condition-specific regulatory maps in Arabidopsis using integrated genomic data (in review)