kamichiotti

kamichiotti's Stars

• igvteam/igv-reports

  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

  Language:Python35253

• VanLoo-lab/gritic

  A tool for timing complex copy number gains in cancer.

  Language:Python124

• ohsu-cedar-comp-hub/WGS-nextflow-workflow

  Language:Nextflow31

• walaj/VariantBam

  Filtering and profiling of next-generational sequencing data using region-specific rules

  Language:Makefile7410

• NCICCGPO/Tumor-Deconvolution-and-Immunogenicity-Manuscript

  Language:R1

• AlexandrovLab/SigProfilerAssignment

  Assignment of known mutational signatures to individual samples and individual somatic mutations

  Language:Python4710

• 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:Python15452

• getzlab/SignatureAnalyzer

  Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.

  Language:Python7321

• 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:Python10137

• 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:Python4613

• epurdom/cancerTiming

  Language:R43

• gerstung-lab/MutationTimeR

  An R package to time somatic mutations

  Language:R6024

• Wedge-lab/battenberg

  Battenberg R package for subclonal copynumber estimation

  Language:R8348

• MD-Anderson-Bioinformatics/MBatch

  Superseded by https://github.com/MD-Anderson-Bioinformatics/BatchEffectsPackage

  Language:R121

• Wedge-lab/dpclust3p

  Dirichlet Process Clustering Pre-Processing Pipeline

  Language:R910

• Wedge-lab/dpclust

  Dirichlet Process based methods for subclonal reconstruction of tumours

  Language:R2916

• broadinstitute/PhylogicNDT

  Language:HTML7139

• PCAWG-11/Evolution

  Code accompanying The Evolutionary history of 2,658 cancers

  468

• gerstung-lab/PCAWG-11

  Code accompanying "The evolutionary history of 2,658 cancers", Nature 578, 122–128 (2020)

  Language:HTML167