Visualization package for Maf Files using Python
0
0
Entering edit mode
7 months ago

Hi!

I am looking for a package similar to Maftools for R but for Python. That is able to take maf fiiles and generate visualizations, survival curves and has the same characteristics as maftools and i can just dowload using python's pip install (without like R, using the biomanager).

(This question arises from the fact that i am using a cluster that contains python image where i can just install packages using pip and for R to install maftools for the current image requires biomanager, but installing biomanager arises several problems related to architecture of the cluster. So just installing in python saves time in this scenario). [EDIT: I have solved this second issue by creating a personalized image for R ,available here https://hub.docker.com/r/msokolovravasqueira/r_studio_genomics/tags ]

Do you have any suggestion?

Best Regards, Manuel

Python maftools Visualization MAF • 692 views
ADD COMMENT
2
Entering edit mode

could be worth posting about your issues with biocmanager in another thread. maybe a solution to that can be found

ADD REPLY
2
Entering edit mode

I second this. OP can you use conda/mamba on the cluster? They precompile the r packages, making them super easy to install. https://anaconda.org/bioconda/bioconductor-maftools

ADD REPLY

Login before adding your answer.

Traffic: 1918 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6