neocaleb/tenetplus

Developed version of TENET using ATAC seq - multiome version (non-multiome version is under construction)

TENETPLUS

A tool for reconstructing Transfer Entropy-based causal gene NETwork from pseudo-time ordered single cell transcriptomic data

multiome version (non-multiome version is under construction)

Citation

Nucleic Acids Research, gkaa1014, https://doi.org/10.1093/nar/gkaa1014 https://github.com/neocaleb/TENET

1. Run TENET using expression data in a csv file and pseudotime result in a text file

Usage

./TENET [expression_file_name] [number_of_threads] [trajectory_file_name] [cell_select_file_name] [history_length]

example

./TENET expression_data.csv 10 trajectory.txt cell_select.txt 1

1-1. Run TENET from TF to target using expression data in a csv file and pseudotime result in a text file

Usage

./TENET_TF [expression_file_name] [number_of_threads] [trajectory_file_name] [cell_select_file_name] [history_length] [species]

example

 ./TENET_TF expression_data.csv 10 trajectory.txt cell_select.txt 1 human

1-2. Run TENET from selected gene peak to target using expression data in a csv file and pseudotime result in a text file

Usage

./TENET_select [expression_file_name] [number_of_threads] [trajectory_file_name] [cell_select_file_name] [history_length] [selcet_list]

example

 ./TENET_select expression_data.csv 10 trajectory.txt cell_select.txt 1 select_list.txt

2 split result matrix (detect peak standard : xxx - xxxx - xxxx)

Usage

sh getMatrix_rowTF_colGN_AB-matrix.sh [TENET result matrix]  
sh getMatrix_rowTF_colPK_C-matrix.sh [TENET result matrix]

example

 sh getMatrix_rowTF_colGN_AB-matrix.sh TE_result_matrix.txt  
 sh getMatrix_rowTF_colPK_C-matrix.sh TE_result_matrix.txt

3 Reconstructing GRN

Usage

python make_GRN_new.py [AB matrix]

example

python make_GRN_new.py TE_result_matrix_rowTF_colGN.txt  
python make_GRN_new.py TE_result_matrix_rowTF_colPK.txt

4 Counting out-degree of a given GRN

Usage

python countOutdegree.py [name of GRN]

Example

python countOutdegree.py TE_result_matrix_rowTF_colGN.sif  
python countOutdegree.py TE_result_matrix_rowTF_colPK.sif

Output file

 TE_result_matrix_rowTF_colPK.sif.outdegree.txt