Comments (7)
marcos-diazg
commented on September 2, 2024
Hi!
First of all, thanks so much for using our app. Regarding your question, can you share with me the maf files you have downloaded from TCGA in order to find a solution? I'm not sure what is going on. It could be due to some dependencies changes in newer versions or also to upgrades in the MAF format. We will try to find a quick solution.
Thanks for letting me know!
from musica.
mwi468
commented on September 2, 2024
Yes Thank you,
That would be very helpful.
Could I have your email to share the files, since they are greater than 10 MB and I am unable to share them on github.
I will just email you a link for my shared dropbox folder
from musica.
marcos-diazg
commented on September 2, 2024
For dropbox is better to use my gmail: [email protected]. Thanks!
from musica.
mwi468
commented on September 2, 2024
Okay thanks I have shared the folder with the files, most of the files are in unzipped format directly from the TCGA and the two unzipped lung cancer MAF files, I was using for analysis
from musica.
marcos-diazg
commented on September 2, 2024
Hi again, I have tested your MAF files and they worked using the specific R version and dependencies specified in the session info I added to the README in 1111aec. This configuration is the same that is present in our web server. In this case the problem is that our server is currently limited to a maximum of 20 samples.
Hope that helps and thanks for your confidence and feedback!
from musica.
mwi468
commented on September 2, 2024
Hi Marcos
I decided to use extractsignatures tool available in MAFtools because I
wanted to continue using R version 3.6 due to some of the other packages in
my pipeline.
I have yet to try the dependencies and packages fthat you had provided for
R 3.4 version and was wondering what would be some of the advantages of
using MuSiCa Vs. the
extracSignatures tool that is part of MAftools
https://www.rdocumentation.org/packages/maftools/versions/0.99.30/topics/extractSignatures
Thanks
…On Thu, Jun 13, 2019 at 11:33 AM Marcos Díaz-Gay ***@***.***> wrote:
Hi again, I have tested your MAF files and they worked using the specific
R version and dependencies specified in the session info I added to the
README in 1111aec
<1111aec>.
This configuration is the same that is present in our web server. In this
case the problem is that our server is currently limited to a maximum of 20
samples.
Hope that helps and thanks for your confidence and feedback!
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#36?email_source=notifications&email_token=ALC2EOMIGD7LTPZJWDDIAZLP2JSENA5CNFSM4HN45X32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXUCYMQ#issuecomment-501754930>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/ALC2EOPGK555H6LDRN36XELP2JSENANCNFSM4HN45X3Q>
.
from musica.
marcos-diazg
commented on September 2, 2024
Hi!
In this case the extractSignatures function of MAFtools allows you to extract a de novo bunch of signatures implicated in the mutational patterns of your samples. However, this approach doesn't allow you to reconstruct your samples using a collection of well-established signatures as it is the case of our MuSiCa application. These are two completely different scenarios. For a more comprehensive explanation you can look at these two recent reviews: Baez-Ortega and Gori, 2019 and Grolleman and Díaz-Gay et al, 2019.
from musica.
Related Issues (20)
- Whole Exome Data HOT 4
- Stopped after clicking "Run" button HOT 4
- Error HOT 3
- Mandatory column names HOT 5
- Downloaded plots have cut off info HOT 3
- Problem uploading maf HOT 1
- Problem Installing ShinySky HOT 5
- To be Updated: `bioclite` with `BiocManager` in dependencies check (repo README.md) HOT 1
- Specify R version to be used HOT 2
- Only somatic mutations and SNVs are supposed to be present in the VCF file? HOT 2
- Input is not detected as bcf or vcf format HOT 6
- Could not identify file types except vcfs HOT 2
- musica_env.yml for conda environmet seems to be Mac specific HOT 10
- Web tool error with MAF file HOT 2
- Interspecies usage HOT 1
- Online analysis failed: Disconnected from the server. HOT 3
- Maf file with multiple samples HOT 3
- Run musica with command line HOT 1
- Online version doesnt work HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from musica.