YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
61 stars 22 forks source link

RI events #90

Closed limeng12 closed 4 years ago

limeng12 commented 6 years ago

Dear author,

I think it's a fantastic idea to use the graph to call alternative splicing events. Do you have plans to continue to maintain and upgrade the software? I ask because I see it hasn't been updated for a long time. I want to use this, but it missed several important AS events, like A5SS, A3SS, RI events, currently only SE and MXE are included. So I think if you can provide some ideas for designing this software. So if you don't have plans to upgrade it, I can add these functions.

Meng

geneyeo commented 6 years ago

Yes we are hoping to maintain and upgrade the software - but if you are interested to contribute to annotate specific events, we can discuss that would be great. Gene Yeo, PhD, MBA Professor Dept of Cellular and Molecular Medicine University of California, San Diego Institute for Genomic Medicine UCSD Stem Cell Program geneyeo@ucsd.edu

Yeo Lab Mailing address: 2880 Torrey Pines Scenic Drive Sanford Consortium for Regenerative Medicine Room 3008, Gene’s Office Room 3805, Wet Lab Room 3114/3115, Bioinformatics Lab La Jolla, CA 92037

Lab website: http://yeolab.github.io

On May 24, 2018, at 9:05 PM, Li meng notifications@github.com wrote:

Dear author,

I think it's a fantastic idea to use the graph to call alternative splicing events. Do you have plans to continue to maintain and upgrade the software? I ask because I see it hasn't been updated for a long time. I want to use this, but it missed several important AS events, like A5SS, A3SS, RI events, currently only SE and MXE are included. So I think if you can provide some ideas for designing this software. So if you don't have plans to upgrade it, I can add these functions.

Meng

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limeng12 commented 4 years ago

Dear authors,

I noticed that this software is built using python, which is not in my programming skillset (R, Java). So I used other software instead. My research interest is analyzing data and splicing, I think maybe I can contribute some codes/ideas if you have some Github/research projects that analyzing datasets in the future. I also hope that the outrigger project can succeed.

Best wishes, Meng