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Cancer Genomics Python Packages

Python packages with the GitHub topic cancer-genomics. Sorted by relevance, with stars and monthly downloads.
AlexandrovLab
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.

19K 121 41
AlexandrovLab
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.

18K 24 3
alexandrovlab
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.

8K 53 15
AlexandrovLab
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.

7K 185 60
uclahs-cds
mopepgen

Multi-Omics Peptide Generator

3K 30 5
AlexandrovLab
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.

2K 185 60
murphycj
agfusion

Python package to annotate and visualize gene fusions.

1K 67 27
kevinhu
cancer-data

Preprocessing for various cancer genomics datasets

918 16 7
AlexandrovLab
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.

860 185 60
BesenbacherLab
lionheart

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

751 11 3
odagayev
cbio-py

This is a python client for the cBioPortal API

653 6 2
bioinform
somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq

652 205 56
Ashford-A
scope-bio

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

389 1 0
BIMSBbioinfo
maui-tools

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

331 50 21
xu62u4u6
pymaftools

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

305 7 2
seandavi
ngcgh

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

245 18 9
cpwardell
fings

Filters for Next Generation Sequencing

227 12 0
mskcc
mimsi

Microsatellite Instability Classification using Multiple Instance Learning

224 28 9
acg-team
str-mut-signatures

Extract STR signatures from annotated VCF

213 0 0
cbg-ethz
scatrex

Map single-cell transcriptomes to copy number evolutionary trees.

205 14 1
AlexandrovLab
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.

144 5 0
AlexandrovLab
new-sigproextractor

Extracts mutational signatures from mutational catalogues

86 185 60
saroudant
sobolev-alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

70 6 2
nicholas-abad
psnv-hunter

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

63 0 1
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