Repositories list

• 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•16•1•Updated Feb 4, 2025Feb 4, 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

  •0•6•36•1•Updated Jan 31, 2025Jan 31, 2025

• Ligare

  Public
  Python

  •

  GNU General Public License v2.0

  •0•1•17•1•Updated Jan 31, 2025Jan 31, 2025

• tool-create-release

  Public
  GitHub reusable workflows to manage the release process

  release-automationgithub-actions

  Python

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

• tool-Nextflow-action

  Public
  Python

  •

  GNU General Public License v2.0

  •0•0•7•2•Updated Jan 27, 2025Jan 27, 2025

• package-NanoStringNorm

  Public
  NanoStringNorm

  R

  •

  GNU General Public License v2.0

  •0•0•1•1•Updated Jan 25, 2025Jan 25, 2025

• package-CancerEvolutionVisualization

  Public
  Publication Quality Phylogenetic Tree Plots

  R

  •

  GNU General Public License v2.0

  •0•2•17•4•Updated Jan 24, 2025Jan 24, 2025

• docker-Delly

  Public
  Docker repository for Delly

  Dockerfile

  •

  GNU General Public License v2.0

  •0•0•1•1•Updated Jan 23, 2025Jan 23, 2025

• package-moPepGen

  Public
  Multi-Omics Peptide Generator

  genomicscancer-genomicsproteomics+ 2proteogenomicsneoantigen

  Python

  •

  GNU General Public License v2.0

  •1•9•20•0•Updated Jan 20, 2025Jan 20, 2025

• docker-SAMtools

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

  docker

  Dockerfile

  •0•0•0•1•Updated Jan 15, 2025Jan 15, 2025

• prostate-cancer-m6a-paper

  Public
  Code for "The Landscape of N6-Methyladenosine in Localized Primary Prostate Cancer"

  R

  •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

• tool-PlantUML-action

  Public
  Shell

  •

  GNU General Public License v2.0

  •0•1•1•3•Updated Jan 13, 2025Jan 13, 2025

• pipeline-call-gSNP

  Public
  Nextflow pipeline to call germline short variants using GATK

  pipelinenextflow

  Nextflow

  •

  GNU General Public License v2.0

  •1•1•22•4•Updated Jan 10, 2025Jan 10, 2025

• package-iSubGen

  Public
  R

  •

  GNU General Public License v2.0

  •0•1•4•0•Updated Dec 27, 2024Dec 27, 2024

• 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•6•0•Updated Dec 26, 2024Dec 26, 2024

• pipeline-recalibrate-BAM

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

  Nextflow

  •

  GNU General Public License v2.0

  •1•1•9•1•Updated Dec 20, 2024Dec 20, 2024

• 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•35•2•Updated Dec 18, 2024Dec 18, 2024

• pipeline-Nextflow-config

  Public
  Set of commonly used Nextflow configs

  Groovy

  •

  GNU General Public License v2.0

  •0•1•16•1•Updated Dec 17, 2024Dec 17, 2024

• pipeline-StableLift

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

  R

  •

  GNU General Public License v2.0

  •0•0•0•1•Updated Dec 17, 2024Dec 17, 2024

• pipeline-call-sSV

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

  pipeline

  Groovy

  •

  GNU General Public License v2.0

  •0•2•17•2•Updated Dec 16, 2024Dec 16, 2024

• 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

  •1•4•25•1•Updated Dec 16, 2024Dec 16, 2024

• pipeline-call-gSV

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

  pipeline

  Nextflow

  •

  GNU General Public License v2.0

  •1•2•10•2•Updated Dec 16, 2024Dec 16, 2024

• pipeline-calculate-targeted-coverage

  Public
  Nextflow pipeline to calculate read-depth related stats for targeted sequencing experiments

  Nextflow

  •

  GNU General Public License v2.0

  •0•0•10•1•Updated Dec 16, 2024Dec 16, 2024

• package-PipeVal

  Public
  An easy to use CLI tool that can be used to validate different parameters in your NF script/pipeline.

  Python

  •

  GNU General Public License v2.0

  •1•5•16•5•Updated Dec 14, 2024Dec 14, 2024

• project-CancerBiology-OutlierAnalysis

  Public
  R

  •

  GNU General Public License v2.0

  •0•1•0•0•Updated Dec 13, 2024Dec 13, 2024

• tool-static-analysis

  Public
  GitHub composite Action to perform static code analysis

  Python

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• megalinter

  Public
  🦙 MegaLinter analyzes 50 languages, 22 formats, 21 tooling formats, excessive copy-pastes, spelling mistakes and security issues in your repository sources with a GitHub Action, other CI tools or locally.

  Dockerfile

  •

  GNU Affero General Public License v3.0

  •244•0•0•0•Updated Nov 26, 2024Nov 26, 2024

• package-VennDiagram

  Public
  Generate High-Resolution Venn and Euler Plots

  R

  •

  GNU General Public License v2.0

  •1•2•6•1•Updated Nov 20, 2024Nov 20, 2024

• tool-NFTest

  Public
  CLI to automate Nextflow pipeline testing

  Python

  •

  GNU General Public License v2.0

  •1•12•13•0•Updated Nov 19, 2024Nov 19, 2024

• package-OutSeekR

  Public
  R

  •

  GNU General Public License v2.0

  •0•0•2•0•Updated Nov 15, 2024Nov 15, 2024