pyscenic

Version:

0.11.2

Category:

bio

Cluster:

Loki

Author / Distributor

https://pyscenic.readthedocs.io/en/latest

Description

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

Documentation

usage: pyscenic [-h] {grn,add_cor,ctx,aucell} ...

Single-CEll regulatory Network Inference and Clustering (0.11.2)

positional arguments:
 {grn,add_cor,ctx,aucell}
                       sub-command help
   grn                 Derive co-expression modules from expression matrix.
   add_cor             [Optional] Add Pearson correlations based on TF-gene expression to the network adjacencies output from the GRN step, and output these to a new adjacencies file. This will normally be
                       done during the "ctx" step.
   ctx                 Find enriched motifs for a gene signature and optionally prune targets from this signature based on cis-regulatory cues.
   aucell              Quantify activity of gene signatures across single cells.

optional arguments:
 -h, --help            show this help message and exit

Examples/Usage

• List available modules:

  $ module avail pyscenic
  

• Load the pyscenic module:

  $ module load bio/pyscenic/0.11.2
  

• Check the loaded modules:

  $ module list
  

• Unload the pyscenic module:

  $ module unload bio/pyscenic/0.11.2
  

• Get help information:

  $ pyscenic --help
  

Installation

Source code is obtained from pyscenic