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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.

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.

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.

structuralvariantannotation

R package designed to simplify structural variant analysis