Repositories list

• public-R-CancerEvolutionVisualization

  Public
  Publication Quality Phylogenetic Tree Plots

  R

  •

  GNU General Public License v2.0

  •0•2•20•2•Updated Jan 23, 2026Jan 23, 2026

• package-ApplyPolygenicScore

  Public
  Utilities for matching a polygenic score coordinate file to a VCF input and the subsequent calculation of the provided polygenic score in each individual.

  R

  •

  GNU General Public License v2.0

  •0•1•8•0•Updated Jan 23, 2026Jan 23, 2026

• public-R-NanoStringNormCNV

  Public
  Helper Functions to Normalize NanoString CNV Data

  R

  •

  GNU General Public License v2.0

  •0•0•0•1•Updated Jan 23, 2026Jan 23, 2026

• package-iSubGen

  Public
  R

  •

  GNU General Public License v2.0

  •0•1•4•1•Updated Jan 23, 2026Jan 23, 2026

• public-R-SeqKat

  Public
  Detection of Kataegis

  R

  •0•0•1•0•Updated Jan 23, 2026Jan 23, 2026

• package-OmicsQC

  Public
  Aggregation of QC metrics and outlier nomination for multi-sample studies

  quality-controlrgenomics+ 2cosine-similarityngs-analysis

  R

  •

  GNU General Public License v2.0

  •0•1•5•1•Updated Jan 23, 2026Jan 23, 2026

• public-R-HistogramZoo

  Public
  HistogramZoo - A set of methods for histogram segmentation and characterization

  R

  •

  GNU General Public License v3.0

  •0•3•35•0•Updated Jan 22, 2026Jan 22, 2026

• package-BoutrosLab-plotting-general

  Public
  Functions to Create Publication-Quality Plots

  R

  •4•16•61•2•Updated Jan 21, 2026Jan 21, 2026

• package-VennDiagram

  Public
  Generate High-Resolution Venn and Euler Plots

  R

  •

  GNU General Public License v2.0

  •2•7•6•2•Updated Jan 14, 2026Jan 14, 2026

• Ligare

  Public
  Python

  •

  GNU General Public License v2.0

  •0•1•16•7•Updated Jan 8, 2026Jan 8, 2026

• tool-PlantUML-action

  Public
  Shell

  •

  GNU General Public License v2.0

  •1•1•1•2•Updated Dec 22, 2025Dec 22, 2025

• tool-create-release

  Public
  GitHub reusable workflows to manage the release process

  release-automationgithub-actions

  Python

  •

  GNU General Public License v2.0

  •1•0•0•3•Updated Dec 15, 2025Dec 15, 2025

• tool-NFTest

  Public
  CLI to automate Nextflow pipeline testing

  Python

  •

  GNU General Public License v2.0

  •2•12•16•3•Updated Dec 15, 2025Dec 15, 2025

• pipeline-StableLift

  Public
  Nextflow pipeline for predicting variant stability across reference genome builds.

  R

  •

  GNU General Public License v2.0

  •1•0•0•2•Updated Nov 24, 2025Nov 24, 2025

• tool-Docker-action

  Public
  An Action to automatically build and push images to the GitHub Container registry. Includes automatic building of images for development.

  dockercicdgithub-actions

  JavaScript

  •

  GNU General Public License v2.0

  •2•0•3•3•Updated Nov 24, 2025Nov 24, 2025

• pipeline-call-sSNV

  Public
  Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.

  pipeline

  Nextflow

  •

  GNU General Public License v2.0

  •3•6•36•5•Updated Nov 24, 2025Nov 24, 2025

• pipeline-call-gSNP

  Public
  Nextflow pipeline to call germline short variants using GATK

  pipelinenextflow

  Nextflow

  •

  GNU General Public License v2.0

  •2•1•21•4•Updated Nov 24, 2025Nov 24, 2025

• metapipeline-DNA

  Public
  Nextflow pipeline to convert BAM to FASTQ, align, perform QC, assess targeted coverage, call gSNP, call sSNV, call mtSNV, call SVs, call sCNA, and perform subclonal reconstruction

  pipeline

  Groovy

  •

  GNU General Public License v2.0

  •1•11•35•1•Updated Nov 24, 2025Nov 24, 2025

• tool-static-analysis

  Public
  GitHub composite Action to perform static code analysis

  Python

  •

  GNU General Public License v2.0

  •1•0•1•2•Updated Nov 24, 2025Nov 24, 2025

• pipeline-call-sSV

  Public
  Nextflow pipeline to call somatic structural variants using DELLY, GRIDSS2 and Manta

  pipeline

  Nextflow

  •

  GNU General Public License v2.0

  •1•2•15•2•Updated Nov 24, 2025Nov 24, 2025

• pipeline-align-DNA

  Public
  Nextflow pipeline to align paired DNA FASTQs and sort, mark duplicates, and index resulting alignment

  pipeline

  Nextflow

  •

  GNU General Public License v2.0

  •2•4•26•3•Updated Nov 24, 2025Nov 24, 2025

• pipeline-call-gSV

  Public
  Nextflow pipeline to call germline structural variants and copy number variants using DELLY and Manta

  pipeline

  R

  •

  GNU General Public License v2.0

  •2•2•11•2•Updated Nov 24, 2025Nov 24, 2025

• pipeline-calculate-mtDNA-CopyNumber

  Public
  Nextflow pipeline to calculate mitochondrial DNA copy number

  Groovy

  •

  GNU General Public License v2.0

  •0•0•0•2•Updated Nov 24, 2025Nov 24, 2025

• pipeline-generate-SQC-BAM

  Public
  Nextflow pipeline to generate sample level QC data from BAM files

  Groovy

  •

  GNU General Public License v2.0

  •0•0•17•3•Updated Nov 24, 2025Nov 24, 2025

• package-moPepGen

  Public
  Multi-Omics Peptide Generator

  genomicscancer-genomicsproteomics+ 2proteogenomicsneoantigen

  Python

  •

  GNU General Public License v2.0

  •5•30•27•1•Updated Nov 6, 2025Nov 6, 2025

• tool-Nextflow-action

  Public
  Python

  •

  GNU General Public License v2.0

  •1•0•6•5•Updated Oct 27, 2025Oct 27, 2025

• package-PrCaMethy

  Public
  R

  •

  GNU General Public License v2.0

  •0•0•1•1•Updated Oct 17, 2025Oct 17, 2025

• project-CancerBiology-OutlierAnalysis

  Public
  R

  •

  GNU General Public License v2.0

  •0•1•0•0•Updated Oct 13, 2025Oct 13, 2025

• package-PCaModelSystemRNA

  Public
  A transcriptomic compendium for a variety of current and upcoming models used to study Prostate cancer.

  rna

  R

  •

  GNU General Public License v2.0

  •0•0•11•3•Updated Sep 8, 2025Sep 8, 2025

• pipeline-recalibrate-BAM

  Public
  Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration

  Nextflow

  •

  GNU General Public License v2.0

  •2•1•14•2•Updated Sep 2, 2025Sep 2, 2025