[ SOFTWARE ]  Mutational signatures-related:

HyperClust by David Mas-Ponte.  https://github.com/davidmasp/hyperclust 

• • A statistical framework to detect clustered mutations in genomes, while accounting for mutation rate heterogenety and for estimated timing of the mutations.  

  • associated with the publication Mas-Ponte & Supek (2020) Nature Genetics "DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers"
    
    

CellLineMutSigs by Jurica Levatić.  https://github.com/jlevatic/CellLineMutSigs  

• • extracting mutational signatures in cancer cell line genomes, and association of mutational signatures with drug activity.  

  • associated with the publication Levatić, Salvadores, Fuster & Supek (2022) Nature Comms "Mutational signatures are markers of drug sensitivity of cancer cells"

[ SOFTWARE ]  Identifying driver mutations:

MutMatch by Elizaveta Besedina.
https://github.com/ebesedina/mutmatch 

• Cancer evolutionary model that was used to identify changes in selection upon copy number alterations (CNA) in cancer genomes

• see publication Besedina & Supek (2024) Nature Comms. Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations.

• uses WES or WGS data for comparative studies of differential selection on cancer genes. 

DiffInvex by Ahmed Khalil.
https://github.com/AISKhalil/diffinvex 

• DiffInvex (Differential Introns-versus-Exons) is an evolutionary model to identify differential selection on point mutations in WGS data between two or more time points/conditions.

• we applied it to comparing treated versus untreated cancer genomes to identify drivers that contribute to chemotherapy resistance: Khalil & Supek (2024) biorxiv.

[ SOFTWARE ]  Machine learning tools:

FastRandomForest2 (beta) by Jordi Piqué Sellés. 

https://github.com/GenomeDataScience/FastRandomForest 

• • A re-implementation of the Random Forest classifier (RF) for the Weka machine learning environment, bringing massive speed and memory use improvements.

[ SOFTWARE ]  Bioinformatics tools:

to be released soon: "Pipeline6" by Daniel Naro

• T2T reference genome-compatible, extensible and scalable pipeline for cancer genomic data processing based on NextFlow

• Includes the gamut of bioinformatics tools from the Hartwig Medical Foundation "Platinum pipeline" (Sage, GRIDSS, PURPLE...) and several additional tools:

• • Strelka2 (SNV, indel calling), Manta (SV calling), Paragraph (germline SV genotyping), Sequenza (CNA calling) GangSTR (repeat indel calling) etc.