index.qmd

# General info {.unnumbered}

This documents is a technical all-in-one documents that contains all the details, code and scripts that are required to replicate the analysis.

Project created using [Quarto](https://quarto.org/), it's installation is recommended before code reproduction.<br>
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](https://www.synapse.org/Synapse:syn53238646). <br>
Files [Cytometry_Panel_for_pipeline.csv](https://www.synapse.org/Synapse:syn53424234) and 
[Samples_Metadata_for_pipeline.csv](https://www.synapse.org/Synapse:syn61406688) should be downloaded to input_data folder.<br>
Folder [Unmixed_Samples_FCS](https://www.synapse.org/Synapse:syn53238692) with unmixed FCS files should be downloaded 
to input_data folder.<br> 
Other folders and files can be generated by scripts or downloaded from Synapse.<br>
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

![](images/Pipeline_scheme.png)