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gitter-lab / SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
MIT License
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Expression data in tab separated text files #11

Open atuldeshpande opened 5 years ago

atuldeshpande commented 5 years ago

Support for compatibility with simple tab-separated text files containing expression data, gene lists and so on, instead of the MAT files currently used.

agitter commented 3 years ago

In our discussion today, one idea for the command line interface would be to have a new shell script to wrap a new MATLAB file that converts .txt files to .mat files. The user would call it like:

bash SINGE_preprocess.sh input_file_list.txt data.mat gene_list.mat

where input_file_list.txt a list of paths to text files with the input data that will be combined into the two .mat files.

Requiring input_file_list.txt is more work for the user than needed. Should we instead use this approach for named parameters in bash scripts? Then, the user could call it like:

bash SINGE_preprocess.sh --expression X.txt --genes gene_list.txt --dataout data.mat --geneout gene_list.mat