mutational-signatures

There are 43 repositories under mutational-signatures topic.

  • AlexandrovLab/SigProfilerExtractor

    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 SigProfilerMatrixGenerator and SigProfilerPlotting.

    Language:Python1532420851

  • ShixiangWang/sigminer

    🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

    Language:R142234618

  • AlexandrovLab/SigProfilerMatrixGenerator

    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.

    Language:Python992613337

  • FunGeST/Palimpsest

    An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.

    Language:R6986119

  • AlexandrovLab/SigProfilerPlotting

    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.

    Language:Python45151413

  • ShixiangWang/sigflow

    Sigflow: Streamline Analysis Workflows for Mutational Signatures, https://github.com/ShixiangWang/sigflow/pkgs/container/sigflow

    Language:R261323

  • AlexandrovLab/SigProfilerMatrixGeneratorR

    R wrapper for utilizing the SigProfilerMatrixGenerator framework

    Language:R202114

  • carjed/helmsman

    highly-efficient & lightweight mutation signature matrix aggregation

    Language:Python192205

  • AlexandrovLab/SigProfilerSimulator

    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.

    Language:Python181164

  • AlexandrovLab/SigProfilerTopography

    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.

    Language:Python171371

  • lrgr/sigma

    SigMa is a probabilistic model for the sequential dependencies of mutation signatures

    Language:Python17727

  • AlexandrovLab/SigProfilerExtractorR

    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 of SigProfilerMatrixGenerator and SigProfilerPlotting.

    Language:R155132

  • XSLiuLab/PC_CNA_signature

    Prostate Cancer Alteration Signature Analysis https://xsliulab.github.io/PC_CNA_signature/

    Language:R12287

  • AlexandrovLab/SigProfilerClusters

    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.

    Language:Python112271

  • AlexandrovLab/SigProfilerPlottingR

    An R wrapper for running the SigProfilerPlotting framework

    Language:R10011

  • ShixiangWang/sigminer.prediction

    Train and Predict Cancer Subtype with Keras Model based on Mutational Signatures

    Language:R8131

  • jessada/pyCancerSig

    Comprehensive cancer signatures with reusable modules written in python, integrating SNV, SV and MSI profiles in signatures decomposed using non-negative matrix factorisation, and produce production ready pdf reports.

    Language:Python7342

  • chrovis/clj-deconstruct-sigs

    deconstructSigs for Clojure

    Language:Clojure41320

  • XUKEREN/phd-pipeline

    Some workflows I wrote for my phd projects

    Language:Shell4100

  • carjed/musigtools

    convenience functions for compatibility between carjed/helmsman output and various mutation signature analysis packages

    Language:R3201

  • edawson/tidysig

    A tidyverse-style package for plotting mutational signatures and context counts.

    Language:R31121

  • marislab/create-pptc-pdx-oncoprints

    As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of these models is required to enable PPTC investigators to develop robust "responder hypotheses" when drug activity is observed. With funding provided by Alex's Lemonade Stand Foundation, we genomically characterize a major subset of 286 PDX models. We use whole exome sequencing, transcriptome sequencing, and SNPArray to characterize the tumor models. The focus on DNA and RNA sequencing data mirrors the current standard practice in most clinical diagnostics lab that use these technologies to detect the spectrum of targetable mutations, gene amplifications, and gene fusion events relevant to preclinical drug development.

    Language:R3502

  • neksa/mutagene

    Python library and package for mutational analysis

    Language:Jupyter Notebook35373

  • nriddiford/mutationProfiles

    Extract and explore snv data

    Language:R3223

  • USCbiostats/HiLDA

    :package: An R package for inferring the mutational exposures difference between groups.

    Language:R3212

  • jennalandy/bayesNMF

    R package implementing Bayesian NMF using various models and prior structures.

    Language:R2201
  • iMutSig

    USCbiostats/iMutSig

    iMutSig: a web application to identify the most similar mutational signature using shiny

    Language:R2640

  • antoine186/convSig

    convSig R Package

    Language:R1200

  • caravagnalab/bascule

    Detecting mutational signatures via bayesian inference and a reference catalog

    Language:R1521

  • caravagnalab/tumourevo

    Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)

    12111

  • catg-umag/bcell-lymphomas-mutational-signatures

    B-Cell Lymphomas Mutational Signatures

    Language:Jupyter Notebook1310

  • dohlee/python-dohlee

    :package: My personal python utility library.

    Language:Python120

  • joanagoncalveslab/SNMF

    SNMF: Integrated Learning of Mutational Signatures and Prediction of DNA Repair Deficiencies by Goossens S, Tepeli YI, Gonçalves JP

    Language:Python1100

  • lrgr/explosig

    ExploSig: web-based interactive visualization of mutation signatures and somatic mutation data

    Language:Vue13932

  • ShixiangWang/absoluteCNVdata

    Pre-compiled absolute CNV data, which can be used for package sigminer/VSHunter and CNV analysis

    105

  • steverozen/PCAWG7-plot-signatures

    Code used to plot mutational signature profiles in https://doi.org/10.1101/322859. Please use the supported R package ICAMS instead.

    Language:R1000