Skip to content

@uclahs-cds UCLA JCCC - Cancer Data Science

Change the repository type filter

All

    Repositories list

    81 repositories

    • 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•10•35•1•Updated Nov 24, 2025Nov 24, 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•2•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

    • tool-PlantUML-action

      Public
      Shell
      •
      GNU General Public License v2.0
      •1•1•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

    • tool-NFTest

      Public
      CLI to automate Nextflow pipeline testing
      Python
      •
      GNU General Public License v2.0
      •2•12•16•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

    • Ligare

      Public
      Python
      •
      GNU General Public License v2.0
      •0•1•16•7•Updated Nov 10, 2025Nov 10, 2025

    • package-moPepGen

      Public
      Multi-Omics Peptide Generator
      genomicscancer-genomicsproteomicsproteogenomicsneoantigen
      Python
      •
      GNU General Public License v2.0
      •5•29•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-CancerEvolutionVisualization

      Public
      Publication Quality Phylogenetic Tree Plots
      R
      •
      GNU General Public License v2.0
      •0•2•20•2•Updated Oct 24, 2025Oct 24, 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

    • docker-BCFtools

      Public
      Dockerfile
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • pipeline-Nextflow-module

      Public
      Set of commonly used Nextflow modules
      Nextflow
      •
      GNU General Public License v2.0
      •1•0•9•1•Updated Aug 28, 2025Aug 28, 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•1•8•0•Updated Aug 20, 2025Aug 20, 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•3•Updated Aug 13, 2025Aug 13, 2025

    • 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•2•Updated Aug 12, 2025Aug 12, 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
      •4•2•3•2•Updated Aug 11, 2025Aug 11, 2025

    • package-BoutrosLab-plotting-general

      Public
      Functions to Create Publication-Quality Plots
      R
      •4•16•61•2•Updated Aug 11, 2025Aug 11, 2025

    • docker-Delly

      Public
      Docker repository for Delly
      Dockerfile
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025