Alexandrov Lab
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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 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…SigProfilerClusters
PublicTool 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.SigProfilerAssignment
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.
- 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.
- SigProfilerPlotting 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.
- An R wrapper for SigProfilerExtractor that 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 o…
HRProfiler
PublicHomologous 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.DupCaller
PublicSigProfilerSimulator
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 point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.DeepHRD
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).
- R wrapper for utilizing the SigProfilerMatrixGenerator framework
SigProfilerAssignmentR
PublicSigProfilerSingleSample
PublicSigProfilerSingleSample 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 for each signature to cause a specific mutation type in the sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.TMB_plotter
PublicSigProfilerSimulatorR
PublicSigProfilerPlottingR
PublicAn R wrapper for running the SigProfilerPlotting framework