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r-bioinformatics / edgePy

A Python implementation of edgeR for differential expression analysis
https://edgepy.readthedocs.io
MIT License
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Data Formats documentation guide #16

Open clintval opened 6 years ago

clintval commented 6 years ago

This appears to need a better description of the formats we are willing to read:

https://github.com/r-bioinformatics/edgePy/blob/master/docs/data-formats.md

julianstanley commented 6 years ago

I'd be happy to try and pick this up if that's alright. At least at the basic level of making the data formats file more pleasing to read. If anyone has any suggestions/comments/requests about what to add, please do let me know!

clintval commented 6 years ago

That would be excellent @julianstanley! Have you worked with edgeR in the past? I have not, so my role has been largely in Python code review and best practice in API design.

@vghorakavi has self-assigned this task. Can you use help @vghorakavi ?

julianstanley commented 6 years ago

I've run the Bowtie/TopHat-htseq-DESeq2 pipeline for RNAseq, but I've never done more than just glance at EdgeR. I can spend some time with the documentation!

And yes, absolutely--I'll defer to whether @vghorakavi needs any help

veena-v-g commented 6 years ago

@julianstanley Thank you so much! I would love to work with you on this issue. You definitely do not need to defer to me. The form of documentation I am familiar with is Word documentation. However, if you have a better idea of what to do, let me know.

eegk commented 6 years ago

Maybe is best to change geneID to featureID, since these methods can be applied to multiple OMICs analyses no. At least, that is my point of view.