aertslab/pyscenic repository overview

⁠pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC_ pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

The pioneering work was done in R and results were published in Nature Methods⁠.

pySCENIC can be run on a single desktop machine but easily scales to multi-core clusters to analyze thousands of cells in no time. The latter is achieved via the dask framework for distributed computing.

Please see also the main pySCENIC repository⁠.

⁠Usage

pySCENIC is available to use with both Docker and Singularity. This can be accomplished in two ways: either using the container as as a portal to the pySCENIC command line interface, or interactively as a Jupyter notebook kernel.

⁠Command line interface

Note that the feather databases, transcription factors, and motif annotation databases need to be accessible to the container. In the below examples, separate mounts are created for the input, output, and databases directories.

To run the pySCENIC CLI via Docker, use the following three steps. A mount point (or more than one) needs to be specified, which contains the input data and necessary resources).

docker run -it --rm \
    -v /data:/data \
    aertslab/pyscenic:0.12.0 pyscenic grn \
        --num_workers 6 \
        -o /data/expr_mat.adjacencies.tsv \
        /data/expr_mat.tsv \
        /data/allTFs_hg38.txt

docker run -it --rm \
    -v /data:/data \
    aertslab/pyscenic:0.12.0 pyscenic ctx \
        /data/expr_mat.adjacencies.tsv \
        /data/hg19-tss-centered-5kb-7species.mc9nr.genes_vs_motifs.rankings.feather \
        /data/hg19-tss-centered-10kb-7species.mc9nr.genes_vs_motifs.rankings.feather \
        --annotations_fname /data/motifs-v9-nr.hgnc-m0.001-o0.0.tbl \
        --expression_mtx_fname /data/expr_mat.tsv \
        --mode "custom_multiprocessing" \
        --output /data/regulons.csv \
        --num_workers 6

docker run -it --rm \
    -v /data:/data \
    aertslab/pyscenic:0.12.0 pyscenic aucell \
        /data/expr_mat.tsv \
        /data/regulons.csv \
        -o /data/auc_mtx.csv \
        --num_workers 6

⁠Website

For more information, please visit LCB⁠ and SCENIC⁠.

⁠License

GNU General Public License v3