Software: kissDE
Description
kissDE is a R package, similar to DEseq, but which works on pairs of variants, and tests if a variant is enriched in one condition. It has been developed to work easily with KisSplice output. It can also work with a simple table of counts obtained by any other means. It requires at least two replicates per condition and at least two conditions.
Available Versions
| Unspecified: | 1.15.3 |
|---|
Docker hub: https://hub.docker.com/r/dwishsan/kissplice-pipeline
Home page: https://kissplice.prabi.fr
Commands
- R
- Rscript
- kissDE.R
Module
You can load the modules by:
module load biocontainers
module load kissde
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run kissde on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=kissde
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers kissde