This project is dedicated for reproducing paper (name and link will be added later) results.
Main purpose of pipeline is to process Cytek FCS unmixed files, clear from data debris, doubles and dead cells, and then divide left cells on types and subtypes for comparing their proportions between age cohorts.

Project created using Quarto, it's installation is recommended before code reproduction.
Folder with name "input_data" should be created in project folder and input data should be downloaded to it from Synapse.

Input and intermediate data can be obtained for Synapse.
Files Cytometry_Panel_for_pipeline.csv and Samples_Metadata_for_pipeline.csv should be downloaded to input_data folder.
Folder Unmixed_Samples_FCS with unmixed FCS files should be downloaded to input_data folder.
Other folders and files can be generated by scripts or downloaded from Synapse.
Pipeline goes as follows:

• data_preprocessing.qmd takes Unmixed_Samples_FCS folder and produce folders Transformed_Samples_FCS and Transformed_Samples_Downsampled_FCS
• expression_processing.qmd takes Transformed_Samples_Downsampled_FCS and produce Intermediate_Pipeline_Files folder
• visualization.qmd takes Intermediate_Pipeline_Files and creates final figures

• Petr Tsurinov - Biolabs