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@uclahs-cds

UCLA JCCC - Cancer Data Science

🏥 Welcome to UCLA JCCC - Cancer Data Science

As “Big Data” researchers, we both apply existing techniques and continuously work to improve them and create new methods. Much of our work to date has focused on prostate cancer, but we are increasingly applying the same techniques to cancers of the kidney, bone and connective tissue (sarcomas), brain, thyroid, ovary and other sites, and discovering fascinating commonalities across them.

Whether you are an external researcher, one of our collaborators, or someone hoping to join our team, we encourage you to use our tools and create issues for any problems you may encounter. Together with your feedback, we can improve our tools and make them more accessible for the next generation of researchers, who will use these techniques to cure cancer and improve human health and well-being in ways we can’t imagine today!

Want to learn more?
Go to the Cancer Data Sciences page where you can read about our recent research areas and some of our recent publications.


📊 Tools

From this organization GitHub page, you can find our R packages

⭐ Most Popular

R Package Description Resources CRAN?
VennDiagram A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, such as two-case scaling, and extensive customization of plot shape and structure. CRAN
BoutrosLab.plotting.general Contains several plotting functions such as barplots, scatterplots, and heatmaps. Also includes functions to combine plots and assist in the creation of these plots. CRAN

💼 Join our team!

To apply, you may either click on the job posting links below, enter the listed job ID on the UCLA Health Recruitment page or UCLA Recruit page for Postdoctoral Fellows, or email Paul at [email protected].

Job Title Job ID Application Link Openings
Dev/Ops Engineer 8012 Apply here! 1
Senior Software Engineer 8534 Apply here! 1
Junior Software Engineer 19691 Apply here! 2
Senior Bioinformatician 8531 Apply here! 3
Scientific Research Associate 4869 Apply here! 1
Assistant to the Director 28907 Apply here! 1
Postdoctoral Fellow JPF07220 Apply here! many

Updated as of October 27, 2022

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  1. package-BoutrosLab-plotting-general package-BoutrosLab-plotting-general Public

    Functions to Create Publication-Quality Plots

    R 12 4

  2. package-VennDiagram package-VennDiagram Public

    Generate High-Resolution Venn and Euler Plots

    R 3 1

  3. package-bedr package-bedr Public

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

    R 3

  4. public-R-NanoStringNormCNV public-R-NanoStringNormCNV Public

    Helper Functions to Normalize NanoString CNV Data

    R

  5. public-R-SeqKat public-R-SeqKat Public

    Detection of Kataegis

    R

  6. package-CancerEvolutionVisualization package-CancerEvolutionVisualization Public

    Publication Quality Phylogenetic Tree Plots

    R 2

Repositories

Showing 10 of 77 repositories
  • 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.

    uclahs-cds/package-ApplyPolygenicScore’s past year of commit activity
    R 0 GPL-2.0 0 6 1 Updated Mar 23, 2025
  • pipeline-call-sSNV Public

    Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.

    uclahs-cds/pipeline-call-sSNV’s past year of commit activity
    Nextflow 6 GPL-2.0 2 35 (1 issue needs help) 0 Updated Mar 22, 2025
  • package-BoutrosLab-plotting-general Public

    Functions to Create Publication-Quality Plots

    uclahs-cds/package-BoutrosLab-plotting-general’s past year of commit activity
    R 12 4 64 (1 issue needs help) 5 Updated Mar 21, 2025
  • pipeline-call-gSV Public

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

    uclahs-cds/pipeline-call-gSV’s past year of commit activity
    Nextflow 2 GPL-2.0 1 11 0 Updated Mar 21, 2025
  • tool-static-analysis Public

    GitHub composite Action to perform static code analysis

    uclahs-cds/tool-static-analysis’s past year of commit activity
    Python 0 GPL-2.0 0 0 0 Updated Mar 21, 2025
  • pipeline-call-gSNP Public

    Nextflow pipeline to call germline short variants using GATK

    uclahs-cds/pipeline-call-gSNP’s past year of commit activity
    Nextflow 1 GPL-2.0 1 21 3 Updated Mar 21, 2025
  • pipeline-align-DNA Public

    Nextflow pipeline to align paired DNA FASTQs and sort, mark duplicates, and index resulting alignment

    uclahs-cds/pipeline-align-DNA’s past year of commit activity
    Nextflow 4 GPL-2.0 1 24 0 Updated Mar 20, 2025
  • Ligare Public
    uclahs-cds/Ligare’s past year of commit activity
    Python 1 GPL-2.0 0 13 (1 issue needs help) 3 Updated Mar 20, 2025
  • pipeline-recalibrate-BAM Public

    Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration

    uclahs-cds/pipeline-recalibrate-BAM’s past year of commit activity
    Nextflow 1 GPL-2.0 1 9 1 Updated Mar 19, 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

    uclahs-cds/pipeline-call-mtSNV’s past year of commit activity
    Nextflow 1 GPL-2.0 0 16 2 Updated Mar 18, 2025