MMSplice predict variant effect on PSI, PSI5, PSI3, splicing efficiency and pathogenicity. This repository contains analysis code for MMSplice manuscript. MMSplice version mmsplice==0.2.0
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The analysis was done with python and ploting was done with R. Required packages are listed in env.yaml.
- Install miniconda or anaconda.
- Run:
conda env create -f env.yaml
. This will install a new conda environmentmmaplice-manuscript
. - Activate the environment:
source activate mmaplice-manuscript
. Run the analysis code (in jupyter-notebooks) in this environment. - Install COSSMO from https://github.com/PSI-Lab/COSSMO
In general, the jupyter-notebooks were used to process, analysis the data and perform predictions. The result table are saved and read by R scripts for plotting.
script/Figure2
: Code to generate figure for the Vex-seq and MFASS data.script/Figure3
: Code to generate figure for GTEx A5SS amd A3SS variants.script/Figure4
: Code to generate figure for MaPSy data.script/Figure5
: Code to generate figure for ClinVar data. Result table of other models were obtained from [Kipoi manuscript] (https://github.com/kipoi/manuscript)data/
: contains raw and processed data