Training dataset for the TRENDY method

<p>This dataset is used for training the TRENDY method for gene regulatory network inference. It also contains the SINC test data set.</p> <p>For a brief description of the code for TRENDY method, see https://github.com/YueWangMathbio/TRENDY.&nbsp;</p> <p>See https://github.com/YueWangMathbio/TRENDY/blob/main/GRN_transformer.pdf for the manuscript of TRENDY method.</p> <p>&nbsp;</p> <p>To use the data:</p> <p>1 download all files from https://github.com/YueWangMathbio/TRENDY</p> <p>2 download all files from this database (both https://zenodo.org/records/14927741 and https://zenodo.org/records/13929908)</p> <p>3 in the folder with all files from GitHub, creat a folder named "total_data_10", and unzip all files with name "dataset....zip" in this folder</p> <p>4 unzip "rev_wendy_all_10.zip" in the folder with all files from GitHub</p> <p>5 unzip "SINC_data.zip", and the files into the folder "SINC"</p> <p>&nbsp;</p> <p>The "total_data_10" folder will contain 102 groups of data, where each group has eight files with different name endings:</p> <p>xxx_A: 1000 ground truth gene regulatory networks, each of size 10*10</p> <p>xxx_cov: 11000 covariance matrices for 1000 samples at 11 time points, each of size 10*10</p> <p>xxx_data: 1000 gene expression samples, each of size 100*10*11 (100 cells, 10 genes, 11 time points)</p> <p>xxx_genie: 10000 inferred gene regulatory networks by GENIE3 method for 1000 samples at 10 time points, each of size 10*10</p> <p>xxx_nlode: 1000 inferred gene regulatory networks by NonlinearODEs method for 1000 samples, each of size 10*10</p> <p>xxx_revcov: 10000 constructed pseudo covariance matrices for 1000 samples at 10 time points, each of size 10*10</p> <p>xxx_sinc:1000 inferred gene regulatory networks by SINCERITIES method for 1000 samples, each of size 10*10</p> <p>xxx_wendy: 10000 inferred gene regulatory networks by WENDY method for 1000 samples at 10 time points, each of size 10*10</p> <p>&nbsp;</p> <p>The "rev_wendy_all_10" folder will contain two&nbsp;groups of data, where each group has eight files with different name endings:</p> <p>xxx_ktstar: 10000 inferred covariance matrices by the first half of TRENDY for 1000 samples at 10 time points, each of size 10*10</p> <p>xxx_revwendy: 10000 inferred gene regulatory networks by the first half of TRENDY for 1000 samples at 10 time points, each of size 10*10</p> <p>&nbsp;</p> <p>The first 100 group with numbering are for training. The one group with "val" is for validation. The one group with "test" is for testing.</p> <p>&nbsp;</p> <p>If you want to train or test new GRN inference methods, then just use the xxx_A files and xxx_data files.</p> <p>&nbsp;</p> <p>&nbsp;</p>