AgfusionPython package to annotate and visualize gene fusions.
Stars: ✭ 36 (-26.53%)
Sv CallersSnakemake-based workflow for detecting structural variants in WGS data
Stars: ✭ 28 (-42.86%)
CbioportalcBioPortal for Cancer Genomics
Stars: ✭ 362 (+638.78%)
PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Stars: ✭ 261 (+432.65%)
civic-clientWeb client for CIViC: Clinical Interpretations of Variants in Cancer
Stars: ✭ 49 (+0%)
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 (+75.51%)
revolverREVOLVER - Repeated Evolution in Cancer
Stars: ✭ 52 (+6.12%)
pathway-mapperPathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Stars: ✭ 47 (-4.08%)
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 (-36.73%)
TeamTeriGenomics using open source tools, running on GCP or AWS
Stars: ✭ 30 (-38.78%)
cpsrCancer Predisposition Sequencing Reporter (CPSR)
Stars: ✭ 44 (-10.2%)
genome-nexusBackend server for Genome Nexus
Stars: ✭ 32 (-34.69%)
mauiMulti-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
Stars: ✭ 42 (-14.29%)
IMPACT-PipelineFramework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
Stars: ✭ 52 (+6.12%)
orchidA novel management, annotation, and machine learning framework for analyzing cancer mutations
Stars: ✭ 29 (-40.82%)
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 (-63.27%)
civic-serverBackend Server for CIViC Project
Stars: ✭ 39 (-20.41%)
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 (+38.78%)
deTiNDeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Stars: ✭ 46 (-6.12%)
SCICoNESingle-cell copy number calling and event history reconstruction.
Stars: ✭ 20 (-59.18%)
cacaoCallable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
Stars: ✭ 21 (-57.14%)
Variants2NeoantigenA neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
Stars: ✭ 27 (-44.9%)
MaftoolsSummarize, Analyze and Visualize MAF files from TCGA or in house studies.
Stars: ✭ 249 (+408.16%)
DellyDELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Stars: ✭ 247 (+404.08%)
Awesome Cancer Variant DatabasesA community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
Stars: ✭ 212 (+332.65%)
IdeogramChromosome visualization for the web
Stars: ✭ 181 (+269.39%)
PcgrPersonal Cancer Genome Reporter (PCGR)
Stars: ✭ 168 (+242.86%)
LollipopsLollipop-style mutation diagrams for annotating genetic variations.
Stars: ✭ 147 (+200%)
LancetMicroassembly based somatic variant caller for NGS data
Stars: ✭ 134 (+173.47%)
Somalierfast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Stars: ✭ 128 (+161.22%)
TybaltTraining and evaluating a variational autoencoder for pan-cancer gene expression data
Stars: ✭ 126 (+157.14%)
SomaticseqAn ensemble approach to accurately detect somatic mutations using SomaticSeq
Stars: ✭ 119 (+142.86%)
Msisensormicrosatellite instability detection using tumor only or paired tumor-normal data
Stars: ✭ 103 (+110.2%)