jh2663

jh2663's Stars

• pineappleEA/pineapple-src

  A former citrus fruit-named emulator's Early Access source code

  Language:C++5.5k1.2k

• GooglingTheCancerGenome/sv-callers

  Snakemake-based workflow for detecting structural variants in genomic data

  Language:Python7435

• im3sanger/dndscv

  dN/dS methods to quantify selection in cancer and somatic evolution

  Language:HTML20947

• raphael-group/decifer

  DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).

  Language:Jupyter Notebook207

• mskcc/facets-suite

  Utility functions for FACETS

  Language:R3325

• marbl/CHM13

  The complete sequence of a human genome

  90599

• lima1/PureCN

  Copy number calling and variant classification using targeted short read sequencing

  Language:R12732

• jokergoo/ComplexHeatmap

  Make Complex Heatmaps

  Language:R1.3k225

• johannesreiter/LiFD

  LiFD is a two-phase algorithm to predict likely functional driver (LiFD) mutations that integrates information from multiple databases and bioinformatic methods.

  Language:Python21

• cancerit/BRASS

  Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.

  Language:Perl5720

• renozao/NMF

  NMF: A Flexible R package for Nonnegative Matrix Factorization

  Language:R13640

• UMCUGenetics/CHORD

  An R package for predicting HR deficiency from mutation contexts

  Language:R267

• eyzhao/hrdetect-pipeline

  Language:R3214

• ait5/CNApp

  CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-friendly interface. The software uses segmented data from either aCGH, SNP-array, whole-exome sequencing or whole-genome sequencing to assess sample profiles and CNA levels, establishing associations with molecular and clinical features. CNApp has three main sections: Re-Seg & Score, Region profile and Classifier model

  Language:R187

• caravagnalab/revolver

  REVOLVER - Repeated Evolution in Cancer

  Language:R6425

• reiterlab/treeomics

  Decrypting somatic mutation patterns to reveal the evolution of cancer

  Language:Python5515

• brentp/mosdepth

  fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

  Language:Nim686100

• shenmskcc/LungIMPACT

  Interactive Shiny application for exploring the lung cancer survival prediction model from the lung IMPACT study.

  Language:R31

• shenmskcc/OncoCast

  Language:HTML55

• FunGeST/Palimpsest

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

  Language:R6819

• keyuan/ccube

  Bayesian mixture models for estimating and clustering cancer cell fractions

  Language:R248

• hdng/clonevol

  Inferring and visualizing clonal evolution in multi-sample cancer sequencing

  Language:R14145

• mskcc/mutation-signatures

  Create mutation signatures from MAF's, and decompose them into Stratton signatures

  Language:R5930

• mskcc/facets

  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

  Language:R13765

• marcjwilliams1/SubClonalSelection.jl

  Inferring selection in cancer sequencing data using ABC and population based simulations

  Language:Julia114

• dariober/cnv_facets

  Somatic copy variant caller (CNV) for next generation sequencing

  Language:R6915