Codes of "Single -cell transcriptomes of zebrafish germline reveal progenitor types and feminization by Foxl2l"

The codes were used in this study "Single -cell transcriptomes of zebrafish germline reveal progenitor types and feminization by Foxl2l".All snapshots of the notebooks for code related to quality control (QC), preprocessing, wild-type (WT) data analysis, integration, public data analysis, mutant (MUT) data analysis, and figure generation are provided in the Notebooks folder. Custom utility functions are located in the Source_codes folder, and the required file lists are available in the File_lists folder.To reproduce the results:Download the raw count matrix from GEO (GSE173718) and perform data preprocessing to obtain the filtered_feature_bc_matrix.Update the path to the filtered_feature_bc_matrix accordingly in the scripts.For the public dataset from Liu et al., download the zx1_40gc_final_orig.robj file and move it to the Data folder.Execute the following notebooks sequentially in the specified order:<br>• 0_QC_Preprocessing.ipynb<br>• 1_WT_data_analysis.ipynb<br>• 2_Integration.ipynb<br>• S_Public_data_analysis.ipynb<br>• S2_MUT_data_analysis.ipynb<br>• 3_Figures.ipynb<br>