Repositories list

• public-R-CancerEvolutionVisualization

  Public
  Publication Quality Phylogenetic Tree Plots

  R

  •

  GNU General Public License v2.0

  •0•2•20•2•Updated Jan 29, 2026Jan 29, 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•3•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•8•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 subcl…

  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