Pinned Repositories
AncHap
Code for analysis of identity-by-descent in genetic data from isolated populations.
AttentionDeepMIL
Implementation of Attention-based Deep Multiple Instance Learning in PyTorch
cookiecutter-reproducible-science
boilerplate for reproducible and transparent science with mybinder integration
DegasperiEtAl-NatureCancer2020-SupplCode
Supplementary Code for Degasperi et al Nature Cancer 2020 paper.
hotspots
A method for finding hotspots of rearrangement breakpoints.
mol_time
R function for calculating the timing of DNA aberration events from NGS data.
PC-CHiP
Pan-Cancer Computational Histopathology
scanbPlots
signature.tools.lib
R package containing useful functions for mutational signature analysis
SigProfilerExtractor
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 in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
DominikGlodzik's Repositories
DominikGlodzik/hotspots
A method for finding hotspots of rearrangement breakpoints.
DominikGlodzik/AncHap
Code for analysis of identity-by-descent in genetic data from isolated populations.
DominikGlodzik/AttentionDeepMIL
Implementation of Attention-based Deep Multiple Instance Learning in PyTorch
DominikGlodzik/cookiecutter-reproducible-science
boilerplate for reproducible and transparent science with mybinder integration
DominikGlodzik/DegasperiEtAl-NatureCancer2020-SupplCode
Supplementary Code for Degasperi et al Nature Cancer 2020 paper.
DominikGlodzik/mol_time
R function for calculating the timing of DNA aberration events from NGS data.
DominikGlodzik/PC-CHiP
Pan-Cancer Computational Histopathology
DominikGlodzik/scanbPlots
DominikGlodzik/signature.tools.lib
R package containing useful functions for mutational signature analysis
DominikGlodzik/SigProfilerExtractor
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 in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
DominikGlodzik/SigProfilerMatrixGenerator
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 file). The tool seamlessly integrates with other SigProfiler tools.
DominikGlodzik/SigProfilerPlotting
SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.
DominikGlodzik/StructuralVariantAnnotation
R package designed to simplify structural variant analysis