ckIGeS-BS

This repository contains IGeS-BS workflow and relevant analysis.

---

Repository Structure

├── IGeS_BS_tool/             # IGeS-BS workflow
	├──  IGeS_Profiling   
	├──  IGeS_BS
	├──  Data	  
	├──  dependency
├── analysis/                 # Scripts used for data preprocessing and constructing IGeS-BS and result analysis
└── README.md                 # Repository documentation

---

Requirements

The scripts and tools in this repository were developed and tested using the following software environment:

• R ≥ 4.0.2 ()the development of IGeS-BS and relevant analysis version)
• openjdk version "1.8.0_372" for running GSEA step

A full list of R library dependencies for environment setup can be found in environment.yml.

IGeS Usage

1. Clone the repository

clone IGeS-BS local folder:

git clone https://github.com/LiHongCSBLab/IGeS_BS.git
cd IGeS_BS_tool

2. Set up the environment

Using Conda (recommended):

conda env create -f environment.yml
conda activate IGeS_BS_env

For checking minimum required dependency, please take a look at: dependency_check.R

3. Run IGeS-profiling

Data dependency

Current profling support two raw data input from LINCS:IGeS-BS

GSE70138:

gene expression profile - GSE70138_Broad_LINCS_Level3_INF_mlr12k_n345976x12328.gctx

*Please download from link below and place under ./IGeS_BS_tool/Data/LINCS_data*

meta info: GSE70138_Broad_LINCS_inst_info.txt (provided in ./Data folder)

GSE92742:

gene expression profile - GSE92742_Broad_LINCS_Level3_INF_mlr12k_n1319138x12328.gctx

*Please download from link below and place under ./IGeS_BS_tool/Data/LINCS_data*

meta info: GSE92742_Broad_LINCS_inst_info.txt (provided in ./Data folder)

Additional annotation files:

gene annotation file: GSE92742_Broad_LINCS_gene_info.txt (provided in ./Data folder)

4. Run IGeS-BS

After profiling for each Compounds, boosting score can be calculated with command-line script.

command-line options:

filepath=/Path/to/IGeS_Profiling_output/
workpath=/Path/to/toolFolder/
savepath=/Path/to/IGeS_BS_output/

Rscript --vanilla plot_for_drug_IGeS.R -a 70138 -c LIHC -t Primary -u TUMERIC -f FALSE \
-d "$filepath}" \
-w "${workpath}" \
-s "${savepath}"> IGeS-BS.log 2>&1&

Data Availability

Due to size constraints, the datasets used in this study are hosted externally. They can be accessed from the following links:

Dataset Description	Link
GSE70138 data	Download from GEO-GSE70138
GSE92742 dataset	Download from GEO-GSE92742
in-house mouse experiment data	[Download from NODE National Omics Data Encyclopedia

Note: Please cite the corresponding data repository when using these datasets in your work.

---

Citation

If you use this code, please cite the following:

[Full citation of the manuscript]

BibTeX:

@article{YourCitationKey,
  title     = {Title of Manuscript},
  author    = {Author Names},
  journal   = {Journal Name},
  year      = {Year},
  doi       = {DOI}
}

---

License

This project is licensed under the [MIT License / GPL-3.0 / Other]. See the LICENSE file for details.

---

Contact

For questions or feedback, please contact:

Li Hong

Email: lihong01@sinh.ac.cn

Affiliation: Shanghai Institute of Nutrition and Health