Processing and Analyzing Mutations and Gene Expression Data in Different Systems.
The present repository is developed within the project directed by Prof. Augusto Gonzalez from the Institute of Cybernetics, Mathematics and Physics, Havana, Cuba. It is aimed at collecting computational tools and data, that hopefully are useful to study mutations and gene expression signatures in different systems.
The repository is released under a GPL version 3 license as stated in the LICENSE file.
The repository is organized in different folders that correspond to several works carried out or being carried on in the group. We specify the reference articles, either by the group or by external authors.
#! Requirements Scripts: Python3 mainly with mathplotlib, numpy, scipy, pylab, xlrd Extra Space: ~73MB for CNV database, ~1GB for TCGA-KIRC database
#! Acronyms and Abbreviations GE : Gene Expression LTEE : Long Term Evolution Experiment MS : Mutation Space CNV : Copy Number Variants CLR : Cancer Lifetime Risk ERS : Extra Risk Score PCA : Principal Component Analysis TCGA : The Cancer Genome Atlas PRAD : Prostate adenocarcinoma KIRC : Kidney renal clear cell carcinoma LUSC : Lung squamous cell carcinoma LUAD : Lung adenocarcinoma UCEC : Uterine Corpus Endometrial Carcinoma KIRP : Kidney renal papillary cell carcinoma BLCA : Bladder Urothelial Carcinoma COAD : Colon adenocarcinoma ESCA : Esophageal carcinoma LIHC : Liver hepatocellular carcinoma STAD : Stomach adenocarcinoma THCA : Thyroid carcinoma BRCA : Breast invasive carcinoma HNSC : Head and Neck squamous cell carcinoma READ : Rectum adenocarcinoma