somatic-variants

There are 70 repositories under somatic-variants topic.

  • luntergroup/octopus

    Bayesian haplotype-based mutation calling

    Language:C++3051926938

  • bioinform/somaticseq

    An ensemble approach to accurately detect somatic mutations using SomaticSeq

    Language:Python194129453

  • bioinform/neusomatic

    NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

    Language:Python168125251

  • 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.

    Language:Python1542221352

  • ShixiangWang/sigminer

    🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

    Language:R147234719

  • google/deepsomatic

    DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

    145113015
  • Sarek

    SciLifeLab/Sarek

    Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

    Language:Nextflow133193247

  • 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.

    Language:Python1012313737

  • PoisonAlien/TCGAmutations

    R data package for pre-compiled somatic mutations from TCGA cohorts and CCLE

    Language:R8951524

  • KChen-lab/Monopogen

    SNV calling from single cell sequencing

    Language:HTML8538218

  • GooglingTheCancerGenome/sv-callers

    Snakemake-based workflow for detecting structural variants in genomic data

    Language:Python7747535

  • HKU-BAL/ClairS

    ClairS - a deep-learning method for long-read somatic small variant calling

    Language:Python756347

  • HKU-BAL/ClairS-TO

    ClairS-TO - a deep-learning method for tumor-only somatic variant calling

    Language:Python503173

  • KarchinLab/2020plus

    Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

    Language:Python49133217

  • 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.

    Language:Python46141413

  • cancerit/dockstore-cgpwgs

    Dockstore implementation of CGP core WGS analysis

    Language:Shell30145714

  • biowdl/germline-DNA

    A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

    Language:WDL248106

  • akiomiyao/tif

    Transposon Insertion Finder - Detection of new TE insertions in NGS data

    Language:Perl20114

  • AlexandrovLab/SigProfilerMatrixGeneratorR

    R wrapper for utilizing the SigProfilerMatrixGenerator framework

    Language:R202114

  • tjbencomo/ngs-pipeline

    Pipeline for Somatic Variant Calling with WES and WGS data

    Language:Python204574

  • 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.

    Language:Python191271

  • carjed/helmsman

    highly-efficient & lightweight mutation signature matrix aggregation

    Language:Python192205

  • AlexandrovLab/SigProfilerSimulator

    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.

    Language:Python18964

  • OpenOmics/genome-seek

    Clinical Whole Genome and Exome Sequencing Pipeline

    Language:Python1811811

  • AlexandrovLab/SigProfilerExtractorR

    An R wrapper for SigProfilerExtractor that 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.

    Language:R155131

  • polyactis/Accucopy

    Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.

    Language:C++152234

  • Sydney-Informatics-Hub/Bioinformatics

    A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

    13201

  • tobiasrausch/nRex

    nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

    Language:Shell12302

  • AlexandrovLab/SigProfilerPlottingR

    An R wrapper for running the SigProfilerPlotting framework

    Language:R10011

  • INMEGEN/Pipelines_INMEGEN

    Flujos de trabajos desarrollados y automatizados en el Inmegen para el procesamiento de datos genómicos y transcriptómicos.

    Language:Nextflow9300

  • akiomiyao/tef

    Transposable Element Finder - Detection of active transposable elements from NGS data

    Language:Perl8120

  • KarchinLab/probabilistic2020

    Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test

    Language:Python81295

  • PoisonAlien/varscan_accessories

    accessory scripts for processing varscan somatic/copynumber outputs.

    Language:Python83310

  • renatopuga/somatico

    GATK 4 Mutect2 Somático

    Language:Shell73033

  • ratschlab/secedo

    Clustering tumor cells based on SNVs from single-cell sequencing data

    Language:C++6830

  • rptashkin/facets2n

    Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

    Language:R6374