In my honest opinion if you are doing biomedical research and you don't have bioinformaticians around and you are not planning to create a whole department it would be better to go for commercial software.
I am a bioinformatician and processing data from let's say RNAseq, DNAseq and ChIPseq would need three different analysis pipelines that even taking into account that you will be using open source existing tools it takes a loooooot of work and time to get everything ready and efficiently working.
About learning the command line, everybody can learn the command line, but you will also need after learning the time to do the work. It is not a thing of a couple of minutes even for a command line ninja. I agree anyway that it will be no bad practice to get a bit into the command line.
There it goes an example of commercial software doing the work for RNAseq and ChIPseq: https://www.integromics.com/products/genomics/ngs/.
No command line and publication ready figures. But this suits for a particular case you will have to find the one for your precise case.
(Don't blame for the ad, yes I work for this enterprise, but I think it is really a constructive example for this discussion)
I am a bioinformatician and processing data from let's say RNAseq, DNAseq and ChIPseq would need three different analysis pipelines that even taking into account that you will be using open source existing tools it takes a loooooot of work and time to get everything ready and efficiently working.
About learning the command line, everybody can learn the command line, but you will also need after learning the time to do the work. It is not a thing of a couple of minutes even for a command line ninja. I agree anyway that it will be no bad practice to get a bit into the command line.
There it goes an example of commercial software doing the work for RNAseq and ChIPseq: https://www.integromics.com/products/genomics/ngs/.
No command line and publication ready figures. But this suits for a particular case you will have to find the one for your precise case.
(Don't blame for the ad, yes I work for this enterprise, but I think it is really a constructive example for this discussion)
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