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welch-lab / liger

R package for integrating and analyzing multiple single-cell datasets
GNU General Public License v3.0
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Is name of this R package liger or rliger? #323

Closed highjws closed 3 weeks ago

highjws commented 3 weeks ago

Hello, I need to install a package named "scCancer" whose dependece pacakge is "liger". When I search this package by the name of "liger", it is your package. However, In your package's DESCRIPTION ,the package name is "rliger". So, I want to know if I got the package wrong—does the scCancer package depend on the liger package that is not the same as yours?

theAeon commented 3 weeks ago

its rliger. would have to look at sccancer as i don't know (but i'm fairly sure liger proper is...not a single cell analysis package)

highjws commented 3 weeks ago

Thanks for your reply! I will check the scCancer package and search for the liger package online. On the other hand, do you know that the R package liger is different from the current one?

theAeon commented 3 weeks ago

all i know about the r package liger is that its completely unrelated

highjws commented 3 weeks ago

Hello, I found the liger package I was looking for; it appears to be related to gene set enrichment functions. Thanks for again! After the issue is resolved, should this comment be closed? I'm a beginner using GitHub.

theAeon commented 3 weeks ago

yeah, you can also close it when you post the comment, like so

highjws commented 3 weeks ago

OK, thanks you very much!

mvfki commented 3 weeks ago

Unfortunately, I just went through their source code. They meant to refer to our package. See this Issue from their repository, which shows you how to get things resolved.

The story is, at the very beginning stage of our package development, we were named by "liger". Due to the fact, which Andrew mentioned, there was already a CRAN released package that occupied this namespace, we had to rename our package to "rliger". scCancer probably introduced our functionality into their package during that time, and NEVER checks if their package still works in full.

Yichen

highjws commented 3 weeks ago

Thanks for for your reply ! So, In summary, scCancer actually uses your package rliger, not any other package , but since the name "liger" was already taken when you developed your package, you changed it to rliger. However, scCancer hasn't updated their dependency from liger to rliger, Is that the overall situation?

mvfki commented 3 weeks ago

Exactly correct

mvfki commented 3 weeks ago

If you really have to use their package and use the option that calls our method, the only two ways are to 1) download their source code and manually change anything "liger" to "rliger", and then install your modified version 2) send them messages or emails and push them to revise their code.

highjws commented 3 weeks ago

Ok, i get. I'm very sorry to have disturbed you; I should have raised the issue under the scCancer project. Sorry for the disturbance, and thank you once again!