The program files (R scripts - files with extension .R) in this repository are licensed under the terms of the GNU General Public License (see LICENSE file). You can redistribute them and/or modify them under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. These programs are distributed in the hope that they will be useful,but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

Each folder has a README file to explain the purpose of each program and output files. The directory organization are inspired by the Cancer Systems Biology groups server organization.

This thesis uses data from 31 cancer types originating from the cancer genome atlas (TCGA), located in the /data. There are three main parts of the analysis:

All the cancer data are used to investigate an appropriate method for handling sample replicates located in /Expression/cancer_type/Technical_replicates.

The breast cancer (BRCA) data set are used to verify a new generated normalization table located. The new table are located in /Expression/get_GLGC_content while the BRCA analysis are performed in /Expression/cancer_type/BRCA_getGLGC and /Expression/cancer_type/DEA_getGLGC

A case study on Uterine Corpus Endometrial Carcinoma (UCEC) are performed with the new pipeline including handling replicates and normalization by the new table in the folder /Expression/cancer_type/Casestudy. Followed up by differential expression, enrichment analysis and visualizations for both UCEC and subtype specific in the subfolders to /Casestudy.