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@uclahs-cds

UCLA JCCC - Cancer Data Science

README.md

🏥 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 pboutros@mednet.ucla.edu.

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 11 4

  2. package-VennDiagram package-VennDiagram Public

    Generate High-Resolution Venn and Euler Plots

    R 2 1

  3. package-bedr package-bedr Public

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

    R 1

  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 72 repositories
  • package-CancerEvolutionVisualization Public

    Publication Quality Phylogenetic Tree Plots

    uclahs-cds/package-CancerEvolutionVisualization’s past year of commit activity
    R 2 GPL-2.0 0 18 6 Updated Nov 26, 2024
  • 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 22 3 Updated Nov 26, 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.

    uclahs-cds/package-ApplyPolygenicScore’s past year of commit activity
    R 0 GPL-2.0 0 7 1 Updated Nov 25, 2024
  • Ligare Public
    uclahs-cds/Ligare’s past year of commit activity
    Python 0 GPL-2.0 0 17 (3 issues need help) 1 Updated Nov 25, 2024
  • pipeline-call-sSV Public

    Nextflow pipeline to call somatic structural variants using DELLY and Manta

    uclahs-cds/pipeline-call-sSV’s past year of commit activity
    Nextflow 1 GPL-2.0 0 18 1 Updated Nov 25, 2024
  • package-PipeVal Public

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

    uclahs-cds/package-PipeVal’s past year of commit activity
    Python 5 GPL-2.0 1 16 4 Updated Nov 23, 2024
  • 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

    uclahs-cds/metapipeline-DNA’s past year of commit activity
    Groovy 4 GPL-2.0 0 37 0 Updated Nov 22, 2024
  • pipeline-call-sSNV Public

    A 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 5 GPL-2.0 0 34 1 Updated Nov 22, 2024
  • package-VennDiagram Public

    Generate High-Resolution Venn and Euler Plots

    uclahs-cds/package-VennDiagram’s past year of commit activity
    R 2 GPL-2.0 1 6 1 Updated Nov 20, 2024
  • megalinter Public Forked from oxsecurity/megalinter

    🦙 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.

    uclahs-cds/megalinter’s past year of commit activity
    Dockerfile 0 AGPL-3.0 245 0 1 Updated Nov 20, 2024
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