hwlim / eeisp_limlab

EEISP

Description

This is a tool for identifying codependent and mutually exclusive gene sets from sparse single-cell RNA-seq data.

Usage

EEISP identifies gene pairs that are codependent and mutually exclusive from sparse scRNA-seq data and takes as input a read count matrix data with rows representing genes and columns representing cells.

How to run EEISP
eeisp.sh performs the calculation of the CDI (Co-Dependency Index) and EEI scores for gene pairs in two steps.

1. eeisp.py calculates the CDI and EEI scores for each gene pair. It outputs lists of gene pairs of CDI and EEI, and the tables of degree distribution.

     * input_file.csv    # An input file forms a comma delimited file (.csv).
     * filename          # A file name of run.
     * --threCDI 10.0    # Set a threshold for CDI which users determine.
     * --threEEI 10.0    # Set a threshold for EEI which users determine.
   

2. gene_name_id.pyconverts to the numbers of CDI and EEI gene pairs to Gene Names (Symbols), if the a list of Ensemble Gene IDs and Gene Names is provided. When only Gene Names (Symbols) is provided, gene_name.py can be performed.

    * genes.tsv        # A list of numbers, Ensemble Gene IDs and Gene Names (or Symbols), which forms a tab delimited file. 
    * <filename>_CDI_score_data_thre10.0.txt      # A list of gene pairs with CDI scores.  
    * <filename>_EEI_score_data_thre10.0.txt      # A list of gene pairs with EEI scores. 
    * <filename>_number_nonzero_exp.txt      　　　# A list of genes that are expressed in more than at least one cell.
    * 10.0             # A threhsold for CDI (or EEI).
   

Installation

EEISP is written in Python3 and does not require an installation.

Example

The sample data is included in sample.

• data.txt The input matrix of scRNA-seq data.

 ## eeisp.sh
 #!/usr/bin/bash

 python3 eeisp.py data.txt Sample --threCDI 0.5 --threEEI 0.5
 python gene_name_id.py Sample genes.tsv Sample_CDI_score_data_thre0.5.txt Sample_EEI_score_data_thre0.5.txt Sample_number_nonzero_exp.txt 0.5

 ## To perform the calculation of CDI and EEI. 
> sh eeisp.sh 

• Output files

   Sample_CDI_score_data_thre0.5.txt            # A list of gene pairs with CDI score.  
   Sample_CDI_degree_distribution_thre0.5.csv   # A table of the number of CDI degree and genes.  
   Sample_CDI_convert_data_thre0.5.txt          # A converted file of the CDI score data.  
   Sample_EEI_score_data_thre0.5.txt            # A list of gene pairs with EEI scores.  
   Sample_EEI_degree_distribution_thre0.5.csv   # A table of the number of EEI degree and genes.   
   Sample_EEI_convert_data_thre0.5.txt          # A converted file of the EEI score data.  

Reference

Nakajima N., Hayashi T., Fujiki K., Shirahige K., Akiyama T., Akutsu T. and Nakato R., Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data., bioRxiv, doi: https://doi.org/10.1101/2021.03.15.435370, 2021.