An ensemble approach to accurately detect somatic mutations using SomaticSeq
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Updated
May 25, 2024 - Python
An ensemble approach to accurately detect somatic mutations using SomaticSeq
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 SigProfilerMatrixGen…
NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
Bayesian haplotype-based mutation calling
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.
Snakemake-based workflow for detecting structural variants in genomic data
GATK 4 Mutect2 Somático
R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)
🌲 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
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
SNV calling from single cell sequencing
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.
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
accessory scripts for processing varscan somatic/copynumber outputs.
Clinical Whole Genome and Exome Sequencing Pipeline
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Run Sentieon pipelines on Google Cloud Platform
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
A Platypus-based variant calling pipeline for cancer data
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