Topic: mutational-signatures Goto Github
Some thing interesting about mutational-signatures
Some thing interesting about mutational-signatures
mutational-signatures,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.
Organization: alexandrovlab
mutational-signatures,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.
Organization: alexandrovlab
mutational-signatures,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.
Organization: alexandrovlab
mutational-signatures,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.
Organization: alexandrovlab
mutational-signatures,R wrapper for utilizing the SigProfilerMatrixGenerator framework
Organization: alexandrovlab
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.
Organization: alexandrovlab
mutational-signatures,An R wrapper for running the SigProfilerPlotting framework
Organization: alexandrovlab
mutational-signatures,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.
Organization: alexandrovlab
mutational-signatures,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.
Organization: alexandrovlab
mutational-signatures,This plot is useful for the comparison of mutational load across the cancer types, with input data in 2 coulmns i.e cancer types and mutatonal load for each samples in specificed cancer type.
User: amarinderthind
mutational-signatures,convSig R Package
User: antoine186
mutational-signatures,Detecting tumor mutational signatures with a CNN
User: beth526
mutational-signatures,Detecting mutational signatures via bayesian inference and a reference catalog
Organization: caravagnalab
Home Page: https://caravagnalab.github.io/basilica/
mutational-signatures,Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
Organization: caravagnalab
mutational-signatures,highly-efficient & lightweight mutation signature matrix aggregation
User: carjed
mutational-signatures,convenience functions for compatibility between carjed/helmsman output and various mutation signature analysis packages
User: carjed
mutational-signatures,B-Cell Lymphomas Mutational Signatures
Organization: catg-umag
mutational-signatures,deconstructSigs for Clojure
Organization: chrovis
mutational-signatures,:package: My personal python utility library.
User: dohlee
Home Page: https://python-dohlee.rtfd.io
mutational-signatures,A somatic mutation signature simulator
User: edawson
mutational-signatures,A tidyverse-style package for plotting mutational signatures and context counts.
User: edawson
mutational-signatures,An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
User: fungest
mutational-signatures,Mutational Signatue Analysis using R
User: hossainlab
mutational-signatures,R package implementing Bayesian NMF using various models and prior structures.
User: jennalandy
mutational-signatures, 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.
User: jessada
mutational-signatures,SNMF: Integrated Learning of Mutational Signatures and Prediction of DNA Repair Deficiencies by Goossens S, Tepeli YI, Gonçalves JP
Organization: joanagoncalveslab
mutational-signatures,ExploSig: web-based interactive visualization of mutation signatures and somatic mutation data
Organization: lrgr
Home Page: https://explosig.lrgr.io
mutational-signatures,SigMa is a probabilistic model for the sequential dependencies of mutation signatures
Organization: lrgr
mutational-signatures,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.
Organization: marislab
mutational-signatures,Python library and package for mutational analysis
User: neksa
Home Page: https://www.ncbi.nlm.nih.gov/projects/mutagene/
mutational-signatures,Extract and explore snv data
User: nriddiford
mutational-signatures,Pre-compiled absolute CNV data, which can be used for package sigminer/VSHunter and CNV analysis
User: shixiangwang
mutational-signatures,Sigflow: Streamline Analysis Workflows for Mutational Signatures, https://github.com/ShixiangWang/sigflow/pkgs/container/sigflow
User: shixiangwang
Home Page: https://hub.docker.com/r/shixiangwang/sigflow
mutational-signatures,🌲 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
User: shixiangwang
Home Page: https://shixiangwang.github.io/sigminer/
mutational-signatures,Train and Predict Cancer Subtype with Keras Model based on Mutational Signatures
User: shixiangwang
mutational-signatures,Shiny server for analyzing mutational signature data; uses mSigAct, ICAMS, and related functionality.
User: steverozen
Home Page: https://msigact.ai
mutational-signatures,Code used to plot mutational signature profiles in https://doi.org/10.1101/322859. Please use the supported R package ICAMS instead.
User: steverozen
mutational-signatures,Algorithms for the generation of substitution matrices from intra-taxa variation data. Implemented and published on human genetic variation data.
User: tairsha
mutational-signatures,:package: An R package for inferring the mutational exposures difference between groups.
Organization: uscbiostats
Home Page: https://bioconductor.org/packages/devel/bioc/html/HiLDA.html
mutational-signatures,iMutSig: a web application to identify the most similar mutational signature using shiny
Organization: uscbiostats
Home Page: https://zhiyang.shinyapps.io/imutsig/
mutational-signatures,Prostate Cancer Alteration Signature Analysis https://xsliulab.github.io/PC_CNA_signature/
Organization: xsliulab
mutational-signatures,Some workflows I wrote for my phd projects
User: xukeren
Home Page: https://xukeren.github.io/phd-pipeline/
mutational-signatures,
User: yangh567
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