Characterisation of HIF-dependent alternative isoforms in pancreatic cancer

Splicing analysis scripts for the paper "Characterisation of HIF-dependent alternative isoforms in pancreatic cancer".

Author

Natalie R. Davidson natalie.davidson@inf.ethz.ch

Requirements

This analysis script was tested on R 3.5.1. External libraries used are: data.table, RColorBrewer, DESeq2, ggplot2, MASS, pheatmap, plyr.

Usage

The script splicing_analysis/differential_splicing.R has 4 command-line parameters.

• indir: The directory containing all spladder result files
• RESULTS_FOLDER: The directory where you would like all differential test result files to be output.
• run_splice_only: TRUE if you would like the analysis to identify HIF dependent splice events that are also independent of expression. FALSE if you would like the events to significantly change in both splicing and expression.
• translation_file: A file which translates which contains two columns ensembl_gene_id to hgnc_symbol.