scRNAClust

This Repository belongs to the RNA Sequence Pipeline for DR.Camila de Souza's Laboratory

This Pipeline follows the following sequential structure

Installation

Please download and run on Python version 3.9.7 and R version 4.0.0 To make use of this Pipeline and it's functionalities please install the latest version of Anaconda

Set up Anaconda Enviroment

conda install -c conda-forge mamba

mamba create -c conda-forge -c bioconda -n rnaPipeline snakemake --file requirements.txt

conda activate rnaPipeline

Install Backspin

conda install -c bioconda backspinpy

Install Giniclust and edit the path in /rnaPipe/giniclust.R to the corresponding Giniclust directory

Install rnaPipe package and its dependancies

CMD R build rnaPipeline

CMD INSTALL rnaPipeline

Execution

run cd Snakemake/<PROCESS TO RUN>

Then execute the desired process with

snakemake --configfile config.yaml -c1

Tests

Test for this software will be done with the LaManno dataset.

LaManno is a light weight single cell RNA sequencing datset, making it convinient for testing.

Please follow the instructions in the exectution with the PATH TO RAW DATA portion in the config file set to ./test/LaManno

Outputs

All outputs are generated to the /output directory

Updating any output or software path can be done within the config.yaml files for each procedure

Example of Analysis Produced