SP_raw_data

Abstract

This repository contains the data and the code used in the StellarPath project and software. A folder can contain the starting raw data in "data", the R scripts in order of execution (op1, op2 ..) and the "output" folder that contains the final processed data of each operation. "External/MIRWALK" contains the processing of the mirwalk database to extract miRNA-targets interactions "External/NETDX_OGD" contains the operations performed to classify the OGD dataset with NetDx "External/NETDX_TCGA" contains the operations performed to classify the TCGA datasets with NetDx interactions "External/NETWORK" contains the preparation of the gene-gene interaction network "External/PATHWAYS" contains the assempbly of the database of pathways from literature "External/RNA-RNA" contains the assembly of the pathways involving non-coding RNA elements "External/TCGA" contains the extraction and preparation of the TCGA datasets "SP1" contains the code used to run StellarPath on TCGA and OGD datasets, plus the code to plot the results included in the publication "StellarPath" contains the R package at the moment of the submission "OGD_tot_RNA" contains the fastq sequences of the total RNA sequencing of the WT samples "OGD_miRNA" contains the fastq sequences of the small RNA sequencing of the WT samples