GRN-IBD

Reference information

https://github.com/aertslab/pySCENIC/blob/master/docs/installation.rst#docker-podman-and-singularity-apptainer-images

Extra required files

Download human feather, TF, and tbl files https://resources.aertslab.org/cistarget/databases/homo_sapiens/

Recommended: Conda environment

For reproducibility, it's recommended to use the environment.yml file provided in this repository. It took sometime to check multiple tools compatibility. The test on the PBMC dataset works well using this environment.

Create environment using environment.yml

mamba env create -f environment.yml

Activate the environment

mamba activate pyscenic_env

Jupyter notebook

To start Jupyter notebook in the server (via browser, to cancel use Ctrl+C): jupyter lab --ip=0.0.0.0 --no-browser

Tutorial

(pySCENIC protocol: PBMC10k downstream analyses)[https://htmlpreview.github.io/?https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_downstream-analysis.html]

Not recommended: Singularity image

Tool is no longer maintained and newer versions of package have several conflicts.

There were two versions of singularity image. pySCENIC CLI version singularity build aertslab-pyscenic-0.12.1.sif docker://aertslab/pyscenic:0.12.1

pySCENIC CLI version + ipython kernel + scanpy singularity build aertslab-pyscenic-scanpy-0.12.1-1.9.1.sif docker://aertslab/pyscenic_scanpy:0.12.1_1.9.1

Running pySCENIC with Singulairity:

To run commands in command line mode using singularity:

singularity run aertslab-pyscenic-0.12.1.sif \
    pyscenic grn \
        -B /data:/data
        --num_workers 6 \
        -o /data/expr_mat.adjacencies.tsv \
        /data/expr_mat.tsv \
        /data/allTFs_hg38.txt