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 (+277.78%)
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 (+377.78%)
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 (+72.22%)
civic-serverBackend Server for CIViC Project
Stars: ✭ 39 (+116.67%)
deTiNDeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Stars: ✭ 46 (+155.56%)
SCICoNESingle-cell copy number calling and event history reconstruction.
Stars: ✭ 20 (+11.11%)
cacaoCallable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
Stars: ✭ 21 (+16.67%)
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.
Stars: ✭ 249 (+1283.33%)
DellyDELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Stars: ✭ 247 (+1272.22%)
Awesome Cancer Variant DatabasesA community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
Stars: ✭ 212 (+1077.78%)
IdeogramChromosome visualization for the web
Stars: ✭ 181 (+905.56%)
PcgrPersonal Cancer Genome Reporter (PCGR)
Stars: ✭ 168 (+833.33%)
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 (+600%)
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.
Stars: ✭ 36 (+100%)
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
Stars: ✭ 47 (+161.11%)
TeamTeriGenomics using open source tools, running on GCP or AWS
Stars: ✭ 30 (+66.67%)
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
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orchidA novel management, annotation, and machine learning framework for analyzing cancer mutations
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