Usage

Usage on Flamingo, the GR's computing cluster

1. make the parameters file according to your needs (configfile: see Configuration section)
2. indicate the path to this file in the path_to_configfile variable
3. run the snakemake command

#parameters
path_to_configfile="<path/to/your_configfile.yaml>"
path_to_pipeline="/mnt/beegfs/pipelines/single-cell/<version>"

#launch
snakemake --profile ${path_to_pipeline}/profiles/slurm -s ${path_to_pipeline}/Snakefile --configfile ${path_to_configfile}

NB: The first utilisation can take some time because of the installation of conda sub-environment (automatic).

Usage on your local machine

1. make the parameters file according to your needs (configfile: see Configuration section)
2. indicate the path to this file in the path_to_configfile variable
3. indicate the path to this pipeline in the path_to_pipeline variable
4. run the snakemake command

#parameters
path_to_configfile="<path/to/your_configfile.yaml>"
path_to_pipeline="<path/to/single-cell>"

#launch
snakemake --profile ${path_to_pipeline}/profiles/local -s ${path_to_pipeline}/Snakefile --configfile ${path_to_configfile}

NB: The first utilisation can take some time because of the installation of conda sub-environment (automatic).

See results on cerebro Application

Cerebro, cell report browser, is an AppShiny which allows users to interactively visualize various parts of single cell transcriptomics analysis without requiring bioinformatics expertise.
At the end of your analysis, you can generate a cerebro object to load it into cerebroApp.

You can use cerebro under R on your local machine:

#to install cerebro:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("romanhaa/cerebroApp")
#to launch cerebro:
cerebroApp::launchCerebro()