Cancer Genomics Python Packages

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.

sigprofilertopography

SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures.

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.

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.

mopepgen

Multi-Omics Peptide Generator

sigproextractor

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.

agfusion

Python package to annotate and visualize gene fusions.

cancer-data

Preprocessing for various cancer genomics datasets

sigpross

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.

lionheart

LIONHEART detects cancer from whole genome sequenced plasma cell-free DNA.

cbio-py

This is a python client for the cBioPortal API

somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq

scope-bio

scOPE: single-cell Oncological Prediction Explorer — transfer-learning from bulk RNA-seq to predict per-cell mutation probabilities in scRNA-seq.

maui-tools

Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit

pymaftools

A Python toolkit for MAF files and multi-omics cancer genomics — parsing, analysis, ML, and publication-ready visualization.

ngcgh

Tools for producing pseudo-cgh of next-generation sequencing data

fings

Filters for Next Generation Sequencing

mimsi

Microsatellite Instability Classification using Multiple Instance Learning

str-mut-signatures

Extract STR signatures from annotated VCF

scatrex

Map single-cell transcriptomes to copy number evolutionary trees.

hrprofiler

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 number features.

new-sigproextractor

Extracts mutational signatures from mutational catalogues

sobolev-alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

psnv-hunter

Comprehensive visualization tool / dashboard to investigate and select Promoter SNVs (pSNVs) for downstream validation