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SigProfilerExtractor
SigProfilerExtractor PublicSigProfilerExtractor 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 i…
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SigProfilerMatrixGenerator
SigProfilerMatrixGenerator PublicSigProfilerMatrixGenerator 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 fil…
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SigProfilerAssignment
SigProfilerAssignment PublicAssignment of known mutational signatures to individual samples and individual somatic mutations
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SigProfilerPlotting
SigProfilerPlotting PublicSigProfilerPlotting 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 oth…
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SigProfilerSingleSample
SigProfilerSingleSample Public archiveSigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability…
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SigProfilerSimulator
SigProfilerSimulator PublicSigProfilerSimulator 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 p…
Repositories
- SigProfilerAssignment Public
Assignment of known mutational signatures to individual samples and individual somatic mutations
AlexandrovLab/SigProfilerAssignment’s past year of commit activity - SigProfilerExtractor Public
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…
AlexandrovLab/SigProfilerExtractor’s past year of commit activity - SigProfilerTopography Public
SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures.
AlexandrovLab/SigProfilerTopography’s past year of commit activity - HRProfiler Public
Homologous Recombination Profiler (HRProfiler) is a classification tool that predicts the HRD probability for both whole-genome and exome-sequenced samples using HRD-specific mutation and copy number features.
AlexandrovLab/HRProfiler’s past year of commit activity - SigProfilerMatrixGenerator Public
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.
AlexandrovLab/SigProfilerMatrixGenerator’s past year of commit activity - EnsembleVariantCallingPipeline Public
The EnsembleVariantCallingPipeline takes files in FASTQ or BAM format and performs SNV and INDEL variant calling from 4 variant callers (Mutect2, Strelka2, Varscan2, MuSE) and indel variant calling from 3 variant callers (Mutect2, Strelka2, Varscan2).
AlexandrovLab/EnsembleVariantCallingPipeline’s past year of commit activity - SigProfilerClusters Public
Tool for analyzing the inter-mutational distances between SNV-SNV and INDEL-INDEL mutations. Tool separates mutations into clustered and non-clustered groups on a sample-dependent basis.
AlexandrovLab/SigProfilerClusters’s past year of commit activity - SigProfilerSimulator Public
SigProfilerSimulator 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.
AlexandrovLab/SigProfilerSimulator’s past year of commit activity - DupCaller_manuscript Public
AlexandrovLab/DupCaller_manuscript’s past year of commit activity