condition-specific regulation
Project description
ConSReg
Condition-specific regulations
Getting Started
1. Installation
1.1 Python installation
ConSReg can be installed from pip:
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:
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPseeker")
Please refer to the instructions described here for more details.
To install CoReg
pakcage from GitHub, type the following commands in R environment:
install.packages("devtools")
library(devtools)
install_github("LiLabAtVT/CoReg")
Please refer to the GitHub page of CoReg
project for more details:
link
To install gglasso
package from CRAN, type the following commands in R environment:
install.pacakges("gglasso")
Please refer to the link here for more details.
To install RRF
package from CRAN, type the following commands in R environment:
install.pacakges("RRF")
Please refer to the link here 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).
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.