Repositories list

• Ligare

  Public
  Python

  •

  GNU General Public License v2.0

  •0•1•13•3•Updated Feb 28, 2025Feb 28, 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•7•35•0•Updated Feb 28, 2025Feb 28, 2025

• tool-Nextflow-action

  Public
  Python

  •

  GNU General Public License v2.0

  •0•0•7•2•Updated Feb 28, 2025Feb 28, 2025

• pipeline-Nextflow-module

  Public
  Set of commonly used Nextflow modules

  Nextflow

  •

  GNU General Public License v2.0

  •0•0•8•1•Updated Feb 27, 2025Feb 27, 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

  •0•0•3•1•Updated Feb 27, 2025Feb 27, 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•5•1•Updated Feb 27, 2025Feb 27, 2025

• package-moPepGen

  Public
  Multi-Omics Peptide Generator

  genomicscancer-genomicsproteomics+ 2proteogenomicsneoantigen

  Python

  •

  GNU General Public License v2.0

  •2•9•24•1•Updated Feb 27, 2025Feb 27, 2025

• package-PrCaMethy

  Public
  R

  •

  GNU General Public License v2.0

  •0•0•1•0•Updated Feb 26, 2025Feb 26, 2025

• pipeline-Nextflow-config

  Public
  Set of commonly used Nextflow configs

  Groovy

  •

  GNU General Public License v2.0

  •0•1•16•1•Updated Feb 25, 2025Feb 25, 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 Feb 25, 2025Feb 25, 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

  •2•6•35•2•Updated Feb 24, 2025Feb 24, 2025

• package-CancerEvolutionVisualization

  Public
  Publication Quality Phylogenetic Tree Plots

  R

  •

  GNU General Public License v2.0

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

• pipeline-call-sSV

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

  pipeline

  R

  •

  GNU General Public License v2.0

  •0•2•18•2•Updated Feb 21, 2025Feb 21, 2025

• pipeline-call-gSNP

  Public
  Nextflow pipeline to call germline short variants using GATK

  pipelinenextflow

  Nextflow

  •

  GNU General Public License v2.0

  •1•1•21•4•Updated Feb 21, 2025Feb 21, 2025

• tool-pypi-publish-action

  Public
  Automatically publish Python packages to PyPI.

  GNU General Public License v2.0

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• 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•11•2•Updated Feb 19, 2025Feb 19, 2025

• package-iSubGen

  Public
  R

  •

  GNU General Public License v2.0

  •0•1•4•1•Updated Feb 18, 2025Feb 18, 2025

• docker-SAMtools

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

  docker

  Dockerfile

  •0•0•0•0•Updated Feb 16, 2025Feb 16, 2025

• package-NanoStringNorm

  Public
  NanoStringNorm

  R

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Feb 13, 2025Feb 13, 2025

• 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•4•Updated Feb 11, 2025Feb 11, 2025

• shim-tool-create-release

  Public
  Repository for UCLA-specific reusuable workflow configuration

  GNU General Public License v2.0

  •0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

• project-CancerBiology-OutlierAnalysis

  Public
  R

  •

  GNU General Public License v2.0

  •0•1•0•0•Updated Feb 7, 2025Feb 7, 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

• 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-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-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-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•24•1•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