single cell merging

[Acribbs]

Hi @AndreasHeger @jscaber I have been developing a single cell pipeline using bus tools and alevin (salmon) for dropseq methods : https://github.com/Acribbs/single-cell/tree/master/pipelines.

I was thinking of merging this pipeline into this repository, however im not entuirely sure what this repository was trying to do as it doesnt contain a pipeline and seems to be an extension to cgat-apps.

Just wondering if each of you could explain the rationale for this repository?

[AndreasHeger]

The idea of this repository was to write wrappers around some SC R packages as a first step to pipelining things. I won't be able to take this much further.

It is a separate repo, as the SC R packages bring in R and a lot of dependencies which we did not want to add to cgat-apps.

[jscaber]

Nothing to add except that I have developed this much further here: https://github.com/jscaber/cgat-proj057 Contains tools for normalising, merging and comparing datasets, differential expression based on zinbwave. Written in the usual CGAT way to keep as generic and broadly applicable as possible (in fact it was a project pipeline once but then I realised quickly how much code was being replicated so rewrote the whole thing while commuting to London...) Jakub Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: Andreas Heger <[email protected]> Sent: Wednesday, March 27, 2019 10:41 pm To: cgat-developers/cgat-singlecell Cc: Jakub Scaber; Mention Subject: Re: [cgat-developers/cgat-singlecell] single cell merging (#3) The idea of this repository was to write wrappers around some SC R packages as a first step to pipelining things. I won't be able to take this much further. It is a separate repo, as the SC R packages bring in R and a lot of dependencies which we did not want to add to cgat-apps. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#3 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ALmOsnqpoIy6ryqtUHD5kXPiQEVmIdzaks5va_OLgaJpZM4b7ppO>.

[Acribbs]

Thanks both for your comments

Ok, well if there isn't any opposition, I wouldn't mind merging my pipeline into this.

@jscaber haha, hope that wasn't a long train journey.