Awesome Cancer Variant DatabasesA community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
Stars: ✭ 212 (-14.17%)
IdeogramChromosome visualization for the web
Stars: ✭ 181 (-26.72%)
PcgrPersonal Cancer Genome Reporter (PCGR)
Stars: ✭ 168 (-31.98%)
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
Stars: ✭ 126 (-48.99%)
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
Stars: ✭ 362 (+46.56%)
PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Stars: ✭ 261 (+5.67%)
civic-clientWeb client for CIViC: Clinical Interpretations of Variants in Cancer
Stars: ✭ 49 (-80.16%)
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 (-65.18%)
revolverREVOLVER - Repeated Evolution in Cancer
Stars: ✭ 52 (-78.95%)
pathway-mapperPathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Stars: ✭ 47 (-80.97%)
SigProfilerPlottingSigProfilerPlotting 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.
Stars: ✭ 31 (-87.45%)
TeamTeriGenomics using open source tools, running on GCP or AWS
Stars: ✭ 30 (-87.85%)
cpsrCancer Predisposition Sequencing Reporter (CPSR)
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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
Stars: ✭ 52 (-78.95%)
orchidA novel management, annotation, and machine learning framework for analyzing cancer mutations
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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.
Stars: ✭ 18 (-92.71%)
civic-serverBackend Server for CIViC Project
Stars: ✭ 39 (-84.21%)
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.
Stars: ✭ 68 (-72.47%)
deTiNDeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Stars: ✭ 46 (-81.38%)
SCICoNESingle-cell copy number calling and event history reconstruction.
Stars: ✭ 20 (-91.9%)
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)
Stars: ✭ 27 (-89.07%)
MaftoolsSummarize, Analyze and Visualize MAF files from TCGA or in house studies.
Stars: ✭ 249 (+0.81%)