SCENIC (R library)

Overview

SCENIC is an R package to infer gene regulatory networks and identify cell states from single-cell RNA-seq data.

The github master branch from 27/06/2018 is installed on the CSF. The version number reflects this date. This is commit id 613781c.

Restrictions on use

Before access can be granted to the software you must read the license terms on the SCENIC website and confirm to us, via email to its-ri-team@manchester.ac.uk, that your work falls within the terms and conditions of that license. We will then add you to the scenic group on the system.

In particular it should be noted that:

• The software is not to be used for commercial purposes.
• You must not copy or make the software available to anyone else.
• You must cite your usage of the software as per the citation information on the SCENIC website.

If you are unsure whether your usage complies with the terms please contact its-ri-team@manchester.ac.uk.

Set up procedure

To access the software you must first load the modulefile:

module load apps/gcc/R-packages/3.4.3/scenic/20180627

This will load the appropriate version of R for you. The version number of scenic indicates the date on which the master branch of the source code repository was downloaded.

Running the application

Please do not run R and scenic on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

R CMD BATCH my_script.R my_script.R.o$JOB_ID
        #
        # -- R must be called with both the "CMD" and "BATCH" options which tell it
        #    to run an R *program*, in this case "my_script.R", instead of presenting
        #    an interactive prompt
        #
        #    library("SCENIC")
        #
        # -- the final argument, "my_test.R.o$JOBID", tells R to send output to a 
        #    file with this name (without, R sends output to "my_test.Rout", which
        #    would be over-written by a second submission of "my_test.R" via
        #    "runmyRjob.qsub")

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• SCENIC website

Updates

None.