Repositories list

• 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

  •2•6•36•1•Updated Jul 23, 2025Jul 23, 2025

• docker-BWA-MEM2

  Public
  Docker repository for BWA-MEM2 and SAMtools

  docker

  Dockerfile

  •0•0•2•1•Updated Jul 23, 2025Jul 23, 2025

• pipeline-recalibrate-BAM

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

  Nextflow

  •

  GNU General Public License v2.0

  •1•1•12•4•Updated Jul 22, 2025Jul 22, 2025

• 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•0•7•1•Updated Jul 22, 2025Jul 22, 2025

• package-moPepGen

  Public
  Multi-Omics Peptide Generator

  genomicscancer-genomicsproteomics+ 2proteogenomicsneoantigen

  Python

  •

  GNU General Public License v2.0

  •4•23•26•1•Updated Jul 22, 2025Jul 22, 2025

• pipeline-call-NonCanonicalPeptide

  Public
  Nextflow pipeline to generate custom databases of non-canonical peptides for proteogenomic analysis

  Nextflow

  •

  GNU General Public License v2.0

  •2•2•3•1•Updated Jul 21, 2025Jul 21, 2025

• package-CancerEvolutionVisualization

  Public
  Publication Quality Phylogenetic Tree Plots

  R

  •

  GNU General Public License v2.0

  •0•2•19•3•Updated Jul 18, 2025Jul 18, 2025

• tool-SMCHet-scoring

  Public
  Automated scoring system for the SMC-Het Challenge

  Python

  •

  Other

  •1•1•0•0•Updated Jul 14, 2025Jul 14, 2025

• tool-Nextflow-action

  Public
  Python

  •

  GNU General Public License v2.0

  •0•0•7•4•Updated Jul 14, 2025Jul 14, 2025

• pipeline-call-mtSNV

  Public
  Nextflow pipeline to detect mitochondrial SNV from normal or tumor BAMs or CRAMs: extracts and remaps mitochondorial reads then calls variants

  pipelinenextflow

  Nextflow

  •

  GNU General Public License v2.0

  •0•1•18•2•Updated Jul 10, 2025Jul 10, 2025

• Ligare

  Public
  Python

  •

  GNU General Public License v2.0

  •0•1•16•2•Updated Jul 9, 2025Jul 9, 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

  •0•2•17•1•Updated Jul 3, 2025Jul 3, 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

  •1•2•11•1•Updated Jul 3, 2025Jul 3, 2025

• package-iSubGen

  Public
  R

  •

  GNU General Public License v2.0

  •0•1•4•1•Updated Jul 1, 2025Jul 1, 2025

• tool-NFTest

  Public
  CLI to automate Nextflow pipeline testing

  Python

  •

  GNU General Public License v2.0

  •1•12•16•0•Updated Jul 1, 2025Jul 1, 2025

• package-BoutrosLab-plotting-general

  Public
  Functions to Create Publication-Quality Plots

  R

  •4•15•60•1•Updated Jun 26, 2025Jun 26, 2025

• tool-R-CMD-check-action

  Public
  GitHub action for checking/testing R packages

  R

  •

  GNU General Public License v2.0

  •0•0•6•1•Updated Jun 20, 2025Jun 20, 2025

• docker-SAMtools

  Public
  Dockerfile for samtools - a tools for "Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format".

  docker

  Dockerfile

  •0•0•1•0•Updated Jun 20, 2025Jun 20, 2025

• package-NanoStringNorm

  Public
  NanoStringNorm

  R

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Jun 19, 2025Jun 19, 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•10•36•0•Updated Jun 18, 2025Jun 18, 2025

• package-VennDiagram

  Public
  Generate High-Resolution Venn and Euler Plots

  R

  •

  GNU General Public License v2.0

  •1•4•6•2•Updated Jun 18, 2025Jun 18, 2025

• public-R-SeqKat

  Public
  Detection of Kataegis

  R

  •0•0•1•1•Updated Jun 18, 2025Jun 18, 2025

• public-R-NanoStringNormCNV

  Public
  Helper Functions to Normalize NanoString CNV Data

  R

  •

  GNU General Public License v2.0

  •0•0•0•1•Updated Jun 18, 2025Jun 18, 2025

• package-OutSeekR

  Public
  R

  •

  GNU General Public License v2.0

  •0•0•2•0•Updated Jun 18, 2025Jun 18, 2025

• package-bedr

  Public
  Genomic Region Processing using Tools Such as `BEDTools`, `BEDOPS` and `Tabix`

  R

  •

  GNU General Public License v2.0

  •3•0•1•0•Updated Jun 18, 2025Jun 18, 2025

• tool-pypi-publish-action

  Public
  Automatically publish Python packages to PyPI.

  GNU General Public License v2.0

  •0•0•0•0•Updated Jun 17, 2025Jun 17, 2025

• 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•0•5•1•Updated Jun 17, 2025Jun 17, 2025

• tool-PlantUML-action

  Public
  Shell

  •

  GNU General Public License v2.0

  •0•1•1•1•Updated Jun 16, 2025Jun 16, 2025

• package-PrCaMethy

  Public
  R

  •

  GNU General Public License v2.0

  •0•0•1•1•Updated Jun 6, 2025Jun 6, 2025

• docker-BCFtools

  Public
  Dockerfile

  •

  GNU General Public License v2.0

  •0•0•1•1•Updated Jun 6, 2025Jun 6, 2025