single_cell_processing

Single-Cell Processing Building Block

This package provides the Single-Cell Processing Building Block (BB).

Table of Contents

• Single-Cell Processing Building Block
  • Table of Contents
  • Description
  • User instructions
    • Requirements
    • Installation
    • Usage
    • Uninstall
  • License
  • Contact

Description

This building block enables the processing and analysis of single-cell RNA-Seq data from each patient in a sample. The first step of the protocol includes quality control, filtering and normalisation of the count matrices at the cellular level. Next, the number of variable genes in each individual is determined and the corresponding scaled matrices are obtained, allowing in the next step the application of dimensionality reduction techniques such as PCA, T-SNE and UMAP.

Finally, cells are clustered using graph-based techniques and annotated to their corresponding cell type, enabling subsequent building blocks to select and work with the set of cells that are relevant to the disease under study (e.g. epithelial cells in COVID19 disease).

User instructions

Requirements

• Python >= 3.6
• Singularity
• permedcoe base package: python3 -m pip install permedcoe

In addition to the dependencies, it is necessary to generate the associated singularity image (single_cell.singularity), located in the Resources folder of this repository.

They MUST be available and exported in the following environment variable before its usage:

export PERMEDCOE_IMAGES="/path/to/images/"

Installation

This package provides an automatic installation script:

./install.sh

Usage

The single_cell_processing_BB package provides a clear interface that allows it to be used with multiple workflow managers (e.g. PyCOMPSs, NextFlow and Snakemake).

It can be imported from python and invoked directly from a PyCOMPSs application, or through the command line for other workflow managers (e.g. Snakemake and NextFlow).

The command line is:

single_cell_processing_BB -d \
    --tmpdir <working_directory> \
    --p_id <p_id> \
    --p_group <p_group> \
    --p_file <p_file> \
    --parallelize <parallelize> \
    --norm_data <norm_data> \
    --raw_data <raw_data> \
    --scaled_data <scaled_data> \
    --cells_metadata <cells_metadata> \
    --outdir <outdir>

Where the parameters are:

	Flag	Parameter	Type	Description
	--tmpdir	<working_directory>	Folder	Working directory (temporary files)
Input	--p_id	<p_id>	String	Patient ID
Input	--p_group	<p_group>	String	Patient's group label
Input	--p_file	<p_file>	File	scRNA-Seq patient's counts
Input	--parallelize	<parallelize>	Integer	Internal parallelism
Output	--norm_data	<norm_data>	File	Normalized counts output filename
Output	--raw_data	<raw_data>	File	Raw counts output filename
Output	--scaled_data	<scaled_data>	File	Scaled counts output filename
Output	--cells_metadata	<cells_metadata>	File	Cells' metadata output filename
Output	--outdir	<outdir>	Folder	Output folder

Uninstall

Uninstall can be achieved by executing the following scripts:

./uninstall.sh
./clean.sh

License

Apache 2.0

Contact

https://permedcoe.eu/contact/

This software has been developed for the PerMedCoE project, funded by the European Commission (EU H2020 951773).