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
•
written
by
Manuel Sokolov Ravasqueira •
0 answers
No answers yet.
Log in to answer this question.
-
Docker image to use Rscript
written by hamarillo •
-
Tutorial: Building Docker images
written by ATpoint
-
OMA not finding numpy; pip and wget failing
written by feander •
-
Can't install DESeq2 via Docker container because of dependency issues
written by cdastmalchi •
-
Using STDIN with BioPython's PDB methods
written by Joe
could be worth posting about your issues with biocmanager in another thread. maybe a solution to that can be found
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