SigProfilerMatrixGeneratorSigProfilerMatrixGenerator 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.
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SigProfilerExtractorSigProfilerExtractor 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…
Stars: ✭ 86 (+177.42%)
SigProfilerSimulatorSigProfilerSimulator 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.
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TeamTeriGenomics using open source tools, running on GCP or AWS
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pitmp-maven-pluginMaven plugin to handle multi module projects for PiTest
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mcoqMutation analysis tool for Coq verification projects
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cpsrCancer Predisposition Sequencing Reporter (CPSR)
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pitest-descartesDescartes supports developers to improve their test suites by reporting weak spots in covered code
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genome-nexusBackend server for Genome Nexus
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mauiMulti-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
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IMPACT-PipelineFramework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
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orchidA novel management, annotation, and machine learning framework for analyzing cancer mutations
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civic-serverBackend Server for CIViC Project
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deTiNDeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
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SCICoNESingle-cell copy number calling and event history reconstruction.
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cacaoCallable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
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Variants2NeoantigenA neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
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2020plusClassifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
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MaftoolsSummarize, Analyze and Visualize MAF files from TCGA or in house studies.
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DellyDELLY2: Structural variant discovery by integrated paired-end and split-read analysis
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Awesome Cancer Variant DatabasesA community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
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IdeogramChromosome visualization for the web
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PcgrPersonal Cancer Genome Reporter (PCGR)
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LollipopsLollipop-style mutation diagrams for annotating genetic variations.
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LancetMicroassembly based somatic variant caller for NGS data
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Somalierfast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
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TybaltTraining and evaluating a variational autoencoder for pan-cancer gene expression data
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SomaticseqAn ensemble approach to accurately detect somatic mutations using SomaticSeq
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Msisensormicrosatellite instability detection using tumor only or paired tumor-normal data
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Music2identifying mutational significance in cancer genomes
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AgfusionPython package to annotate and visualize gene fusions.
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Sv CallersSnakemake-based workflow for detecting structural variants in WGS data
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CbioportalcBioPortal for Cancer Genomics
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PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
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civic-clientWeb client for CIViC: Clinical Interpretations of Variants in Cancer
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revolverREVOLVER - Repeated Evolution in Cancer
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pathway-mapperPathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
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InfectionPHP Mutation Testing library
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