/Sciacovelli_et_al

Code of paper Sciacovelli et al. Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition, Nature, 2016

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition

Sciacovelli et al., 2016, Nature analysis files:

file description
de_proteomics.r Differential protein abundance script, using limma bioconductor package
gsea_enrichment.py GSEA analysis of EMT + MSigDB signature in mouse and human samples
preprocess_proteomics.py Workflow followed to process the mass-spectrometry proteomics of mouse and human samples
tcga_rnaseq_correlations.py Correlation analysis of the TCGA KIRC tumour samples
volcanos.py Script used to generate the volcano plots
kirp_*.r Worflow for differential expression analysis of KIRP RNA-seq TCGA samples
preprocess_rnaseq.py Preprocessing steps to parse the raw counts from the RNA-seq samples
rnaseq_limma.r Workflow for differential expression analysis of human and mouse RNA-seq samples