iDEP (integrated Differential Expression and Pathway analysis) is shiny application for analyzing RNA-seq data. A public instance is available at http://bioinformatics.sdstate.edu/idep/ and on this page we show how an ephemeral instance can be run locally on compute nodes.
iDEP reads in gene-level expression data (read counts or FPKM), performs exploratory data analysis (EDA), differential expression, pathway analysis, biclustering, and co-expression network analysis. iDEP also accepts DNA microarray data or other gene-level expression data, such as those from Chip-seq or proteomics studies.
This is best done in an sinteractive job. Please do not let an idle iDEP session linger. Shut down your instance when you are done with the analysis. Note that iDEP requires lscratch.
sinteractive can help setting up tunnels to access the idep instances on the compute node (see here for more detail).
For this example we will allocate an interactive session and start an iDEP instance as shown below. First, we launch tmux (or screen) on the login node so that we don't lose our session if our connection to the login node drops.
[user@biowulf]$ module load tmux # You can use screen instead; you don't need to module load it
[user@biowulf]$ tmux
[user@biowulf]$ sinteractive --mem=16g --cpus-per-task=2 --gres=lscratch:20 --tunnel
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
Created 1 generic SSH tunnel(s) from this compute node to
biowulf for your use at port numbers defined
in the $PORTn ($PORT1, ...) environment variables.
Please create a SSH tunnel from your workstation to these ports on biowulf.
On Linux/MacOS, open a terminal and run:
ssh -L 33327:localhost:33327 biowulf.nih.gov
For Windows instructions, see https://hpc.nih.gov/docs/tunneling
[user@cn3144]$ module load idep
[user@cn3144]$ idep-server
Loading required package: shiny
Listening on http://127.0.0.1:33327
Keep this running for as long as you are using iDEP. Note the port number and the compute node which are required to connect to your iDEP instance.
Connecting to your iDEP instance on a compute node with your local browser requires setting up the second leg of the tunnel (from your computer to biowulf) and connecting it to the tunnel from biowulf to the compute node. This is described in detail on our tunneling page.
Once the tunnel has been established, you can visit the interface of the iDEP
shiny app at http://localhost:33327/idep/ (replacing 33327 with the
port used by your instance of idep-server).