Homologous Recombination Profiler (HRProfiler) is a classification tool that predicts the HRD probability for both whole-genome and exome-sequenced samples using HRD-specific mutation and copy numb…

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

Personal Cancer Genome Reporter (PCGR)

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED fil…

Annotation and Ranking of Structural Variation

Course material for the EMBL-EBI Introduction to Bioinformatics course

Scripts from the "Scaling things up" talk I gave at the yearly EBI NGS Bioinformatics course between 2019 and 2024.

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities i…

ASCAT R package

Tumor Mutational Burden

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing