Code utilised for my (Jacobo Solorzano) Thesis manuscript
Table of Contents
this GitHub repo summarises the code used during my PhD.
The main structure match that of the manuscript:
- PDX stroma analysis: from the initial assessment of cell type proportions or transcription factor activities to the ICA and the posterior analysis. A second readme with details regarding this section can be found here.
For any quick correlation analysis, I created 08_Check_quick_Corrs, which can produce correlations of any of the stromal/tumour components with Stroma/Tumour gene expression
- ISRact projection: this includes all the efforts carried out to detect ISRact in transcription. This includes the generation of ISRactPCA but also the usage of the Molecular signature generator to produce ISRactICA, a novel classifier not included in the thesis. A second readme with the details regarding this section can be found here.
In both detailed documents the results of each section and figures, connected to the scripts that produce them is indicated for easy tracking.
Distributed under the MIT License. See LICENSE.txt for more information.
Jacobo Solorzano - [email protected]
Project Link: https://github.com/VeraPancaldiLab/TRANSDUCER