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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
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Add converter from Seurat object to cbBuild compatible tsv #37

Closed mxposed closed 6 years ago

mxposed commented 6 years ago

Hi

This is a basic script to convert Seurat objects to tsv files compatible with cbBuild. Please, let me know what you think, and what I should add to this to be more in line with cbScanpy for instance. Also I would appreciate suggestions on how to handle cellbrowser.conf

maximilianh commented 6 years ago

Awesome!! Many thanks for this! I was just starting to work in it so this is perfect timing! I'll look into it next week.

maximilianh commented 6 years ago

This is great. Do you know how we could make a little library for R ? In this way, people could export their R objects directly from the R command line and wouldn't have to drop in the Linux command line. Is it enough just to create an R file and ask people to load it? Sorry, I'm not very good at R...

mxposed commented 6 years ago

Hi! I’ll look into creating a small library out of this script soon, will send you another pull request

maximilianh commented 6 years ago

Wow, many thanks!

maximilianh commented 6 years ago

Hi Nikolai, I would like to rename cbSeurat to something else, as I would like to write a new program cbSeurat, that, like cbScanpy, takes an expression matrix and runs it through a quick-and-dirty Seurat pipeline based on the Seurat tutorial and creates the cellbrowser.conf file for it. Is that OK with you? Do you have a preference on the name, e.g. cbSeuratToTsv or cbSeuratImport or something like that?

mxposed commented 6 years ago

Hi. All right, sure, go ahead. I don't have any particular preference. I guess it would be logical if workflows for scanpy and seurat would be parallel

mxposed commented 6 years ago

Hey. I've found this tiny recipe for creating a package: https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/

Should I follow this? In a separate folder in this repository or in a separate repository? What do you think?

maximilianh commented 6 years ago

Hi, wait, before you spend time on this, shouldn't we add the Seurat folks if they want to add your function to Seurat? That would be very useful... then people wouldn't have to install anything!

On Thu, Oct 11, 2018 at 3:27 PM Jay Bird notifications@github.com wrote:

Hey. I've found this tiny recipe for creating a package: https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/

Should I follow this? In a separate folder in this repository or in a separate repository? What do you think?

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/pull/37#issuecomment-428997640, or mute the thread https://github.com/notifications/unsubscribe-auth/AAS-TYriQfuTF3NSbcniPZZOYCAB3rcfks5uj2NlgaJpZM4W7mXg .

maximilianh commented 6 years ago

You can create the pull request (which means you'll get the visibility and attribution for what is your code) or I can do the pull request (if you're busy at the moment) and point out that it really is your code and acknowledge you in the cellbrowser docs.

On Sat, Oct 13, 2018 at 3:15 PM Maximilian Haeussler maximilianh@gmail.com wrote:

Hi, wait, before you spend time on this, shouldn't we add the Seurat folks if they want to add your function to Seurat? That would be very useful... then people wouldn't have to install anything!

On Thu, Oct 11, 2018 at 3:27 PM Jay Bird notifications@github.com wrote:

Hey. I've found this tiny recipe for creating a package: https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/

Should I follow this? In a separate folder in this repository or in a separate repository? What do you think?

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/pull/37#issuecomment-428997640, or mute the thread https://github.com/notifications/unsubscribe-auth/AAS-TYriQfuTF3NSbcniPZZOYCAB3rcfks5uj2NlgaJpZM4W7mXg .

mxposed commented 6 years ago

Great idea, I haven't thought about that. I'll ask Seurat folks