SCENIC<\/a> is an R package to infer gene regulatory networks and identify cell states from single-cell RNA-seq data.<\/p>\n The github master branch from 27\/06\/2018 is installed on the CSF. The version number reflects this date. This is commit id 613781c.<\/p>\n Before access can be granted to the software you must read the license terms on the SCENIC website<\/a> 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 In particular it should be noted that:<\/p>\n If you are unsure whether your usage complies with the terms please contact its-ri-team@manchester.ac.uk.<\/p>\n To access the software you must first load the modulefile:<\/p>\n This will load the appropriate version of R for you. The version number of scenic indicates the date on which the master<\/em> branch of the source code repository was downloaded.<\/p>\n Please do not run R and scenic on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" 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.. Read more »<\/a><\/p>\n","protected":false},"author":15,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4758","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4758","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/15"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=4758"}],"version-history":[{"count":4,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4758\/revisions"}],"predecessor-version":[{"id":4771,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4758\/revisions\/4771"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=4758"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
scenic<\/code> group on the system.<\/p>\n\n
Set up procedure<\/h2>\n
\r\nmodule load apps\/gcc\/R-packages\/3.4.3\/scenic\/20180627\r\n<\/pre>\n
Running the application<\/h2>\n
Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n\r\nR CMD BATCH my_script.R my_script.R.o$JOB_ID\r\n #\r\n # -- R must be called with both the \"CMD\" and \"BATCH\" options which tell it\r\n # to run an R *program*, in this case \"my_script.R\", instead of presenting\r\n # an interactive prompt\r\n #\r\n # library(\"SCENIC\")\r\n #\r\n # -- the final argument, \"my_test.R.o$JOBID\", tells R to send output to a \r\n # file with this name (without, R sends output to \"my_test.Rout\", which\r\n # would be over-written by a second submission of \"my_test.R\" via\r\n # \"runmyRjob.qsub\")\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Further info<\/h2>\n
\n
Updates<\/h2>\n