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Search results for python cancer genomics

cancer-genomics x

26 search results found

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Somaticseq ⭐ 185

An ensemble approach to accurately detect somatic mutations using SomaticSeq

Sigprofilerextractor ⭐ 132

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 ⭐ 91

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.

Sv Callers ⭐ 52

Snakemake-based workflow for detecting structural variants in genomic data

Agfusion ⭐ 46

Python package to annotate and visualize gene fusions.

Sevenbridges Python ⭐ 44

SevenBridges Python Api bindings

Sigprofilerplotting ⭐ 43

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.

Sigprofilersimulator ⭐ 18

SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

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

Umccrise ⭐ 14

🐍 DRAGEN Tumor/Normal workflow post-processing

Ampliconreconstructorom ⭐ 14

Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data

Sigprofilertopography ⭐ 13

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.

Microsatellite Instability Classification using Multiple Instance Learning

Cancer_data ⭐ 11

A unified downloader+preprocessor for cancer genomics datasets

Map single-cell transcriptomes to copy number evolutionary trees.

Canceromicsnet ⭐ 10

A Graph Neural Network Model for prediction of the effectiveness of a drug on a given cancer cell lines

The Broad Institute Single Cell Rna Seq Data Set ⭐ 9

Visualize cancer genomes with FAIR single-cell RNA-seq data

The first GANs-based omics-to-omics translation framework

Sigprofilerclusters ⭐ 8

Tool for analyzing the inter-mutational distances between SNV-SNV and INDEL-INDEL mutations. Tool separates mutations into clustered and non-clustered groups on a sample-dependent basis.

Multimodal Autoencoder For Breast Cancer ⭐ 7

Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data

Access Pipeline ⭐ 7

cfDNA Sequencing Pipeline with UMI

Gsinghal_python_src ⭐ 6

Python Code, Machine Learning, Cancer Genomics, DNA/RNA Sequence Analysis

Filters for Next Generation Sequencing

Cbpmanager ⭐ 5

Generate, manage and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics.

CG - cancer genomics pipeline

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