Entering edit mode
2.7 years ago
liorglic
★
1.5k
Are there any recommended command line tools for differential gene expression analysis? I am looking for alternatives to the common R packages such as DESeq2, EdgeR, and Limma-Voom.
I know that these are considered "state of the art", but I am teaching a course about NGS data analysis and I'd like to try and avoid teaching any programming. I am willing to compromise analysis quality in favor of simplicity.
Any ideas?
Maybe https://usegalaxy.org ?
Thanks, I was looking for a Linux-based tool, and AFAIK, there is no easy way to run Galaxy tools locally.
I think it is fundamentally wrong to teach inferior tools for the sake of simplicity. You cannot do proper analysis with this, so people should not get used to it. OMICS these days without basic R or coding skills does not work. Just my two cents... DESeq2 is really not difficult to use, the manual covers all standard analysis.
So, first, I am pretty sure I don't understand the question, because I can't see why using the command line would obviate coding skill, while using something like RStudio would not... So, there is a chance I am missing the point here.
Having said that, I see no reason why you couldn't just call the "state of the art" scripts from the command line ...
What is wrong with:
where this script contains something like:
Why would that be any different than calling a worse algorithm using the command line? You can still feed-in arguments (e.g. a flatfile containing locations of data and metadata) ? Sorry if I'm being dense.