somatic-variants
There are 3 repositories under somatic-variants topic.
luntergroup / octopus
Bayesian haplotype-based mutation calling
Language:C++ 297bioinform / somaticseq
An ensemble approach to accurately detect somatic mutations using SomaticSeq
Language:Python 190NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
Language:Python 167AlexandrovLab / 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:Python 146ShixiangWang / 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:R 137- Sarek
SciLifeLab / Sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Language:Nextflow 132 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:Python 95google / deepsomatic
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
PoisonAlien / TCGAmutations
R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)
Language:R 76GooglingTheCancerGenome / sv-callers
Snakemake-based workflow for detecting structural variants in genomic data
Language:Python 71- Language:HTML 63
- Language:Python 56
KarchinLab / 2020plus
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
Language:Python 48SigProfilerPlotting 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:Python 45- Language:Python 32
cancerit / dockstore-cgpwgs
Dockstore implementation of CGP core WGS analysis
Language:Shell 28biowdl / germline-DNA
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
Language:WDL 23R wrapper for utilizing the SigProfilerMatrixGenerator framework
Language:R 20- Language:Perl 19
- Language:Python 19
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:Python 18tjbencomo / ngs-pipeline
Pipeline for Somatic Variant Calling with WES and WGS data
Language:Python 17OpenOmics / genome-seek
Clinical Whole Genome and Exome Sequencing Pipeline
Language:Python 16An 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:R 15SigProfilerTopography 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:Python 15polyactis / Accucopy
Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.
Language:C++ 14Sydney-Informatics-Hub / Bioinformatics
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
tobiasrausch / nRex
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
Language:Shell 11An R wrapper for running the SigProfilerPlotting framework
Language:R 10akiomiyao / tef
Transposable Element Finder - Detection of active transposable elements from NGS data
Language:Perl 8Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test
Language:Python 8accessory scripts for processing varscan somatic/copynumber outputs.
Language:Python 8INMEGEN / Pipelines_INMEGEN
Flujos de trabajos desarrollados y automatizados en el INMEGEN para el procesamiento de datos genómicos y transcriptómicos.
Language:Nextflow 7renatopuga / somatico
GATK 4 Mutect2 Somático
Language:Shell 7- Language:C++ 6
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:R 6
