config.yaml

# This theme is derived from hugo-fresh
# https://themes.gohugo.io/hugo-fresh/
baseURL: https://facileverse.netlify.com/
languageCode: en-us
title: "facile.bio: interactive tools for genomics analysis"
theme: facileverse
# publishDir: "../facileverse.github.io"
ignoreFiles: ["\\.Rmd$", "\\.Rmarkdown$", "_files$", "_cache$"]
params:
  navbarlogo:
  # Vector Illustration by <a rel="nofollow" href="https://vecteezy.com">www.vecteezy.com</a>
  # Logo (from static/images/logos/___)
   image: logos/facile.svg
   link: /
  font:
    name: "Open Sans"
    sizes: [400,600]
  hero:
    # Main hero title
    title: inteRact with science
    # Hero subtitle (optional)
    subtitle: >
      facile.bio is an ecosystem of R packages that provides modular building
      blocks for the interactive analysis of genomics data.
    # Button text
    buttontext: Get Started
    # Where the main hero button links to
    buttonlink: "https://facilebio.github.io/FacileAnalysis/articles/FacileAnalysis-RNAseq.html"
    # Hero image (from static/images/___)
    image: illustrations/worker.svg
    # Footer logos (from static/images/logos/clients/___.svg)
    # clientlogos:
    # - systek
    # - tribe
    # - kromo
    # - infinite
    # - gutwork
  # Customizable navbar. For a dropdown, add a "sublinks" list.
  navbar:
  - title: Articles
    sublinks:
    - title: "RNA-seq analysis: the facile way"
      url: https://facilebio.github.io/FacileAnalysis/articles/FacileAnalysis-RNAseq.html
    - title: The FacileData API
      url: /
  - title: Packages
    sublinks:
    - title: FacileData
      url: https://facilebio.github.io/FacileData/
    - title: FacileAnalysis
      url: https://facilebio.github.io/FacileAnalysis/
    - title: FacileBiocData
      url: https://facilebio.github.io/FacileBiocData/
    - title: FacileShine
      url: https://facilebio.github.io/FacileShine/
    - title: FacileViz
      url: https://facilebio.github.io/FacileViz/
  - title: Datasets
    sublinks:
    - title: Build Your Own
      url: https://facilebio.github.io/FacileData/articles/FacileDataSet-assembly.html
    - title: FacileTcgaDataSet
      url: https://facilebio.github.io/FacileTcgaDataSet/
    - title: FacileRecountDataSet
      url: /
    - title: FacileArchs4DataSet
      url: https://facilebio.github.io/FacileArchs4DataSet/
  - title: GitHub
    url: https://github.com/facilebio/
  #section1:
  #  title: Analyze without analyzing
  #  subtitle: Simplifeid and consistent APIs for data retrieval and analysis lower the barriers to bioinformatic analyses
  #  tiles:
  #  - title: App builder
  #    icon: mouse-globe
  #    text: This is some explanatory text that is on two rows
  #    url: /
  #    buttonText: Free trial
  #  - title: Cloud integration
  #    icon: laptop-cloud
  #    text: This is some explanatory text that is on two rows
  #    url: /
  #    buttonText: Get started
  #  - title: Add-ons & plugins
  #    icon: plug-cloud
  #    text: This is some explanatory text that is on two rows
  #    url: /
  #    buttonText: Get started
  section2:
    title: Core Packages
    subtitle: They even have unit tests!
    features:
    - title: FacileData
      text: >
        Defines a "tidy-like" API for data query and retrieval from a
        multi-assay datastore. Provides a reference implementation
        (`FacileDataSet`) that enables the analysis of large, out-of-memory
        datasets by using SQLite to store subject-, sample-, and assay-level
        metadata, and HDF5 to store dense high-dimensional assay data.
      icon: laptop-globe
      url: https://facilebio.github.io/FacileData/
    - title: FacileBiocData
      text: >
        Implements the facile API over standard bioconductor assay containers.
      icon: mouse-globe
      url: https://facilebio.github.io/FacileBiocData/
    - title: FacileAnalysis
      text: >
        Provides modular analysis workflows for common analysis tasks, like
        PCA, differential expression, and gene set enrichment analysis. A common
        set of methods are defined (`shine()`, `viz()` and `report()`) to
        provide interactive views over these results, which can be placed into a
        shiny application or embedded into an Rmarkdown report.
      icon: doc-sync
      url: https://facilebio.github.io/FacileAnalysis/
    - title: FacileShine
      text: Provides shiny components to interact with and retrieve data from a facile datastore.
      icon: mobile-feed
      url: https://facilebio.github.io/FacileShine/
    - title: FacileViz
      text: Provides interactive (in the javascript sense) views over a facile datastore (scatterplots, boxplots, etc.)
      icon: mouse-globe
      url: https://facilebio.github.io/FacileViz/
  #section3:
  # mainly a screenshot of the application
  #  title: One platform
  #  subtitle: To rule them all
  #  image: illustrations/mockups/app-mockup.png
  #  buttonText: Get started
  #  buttonLink: "#"
  #section4:
  # orange section with customer testimonial quotes
  #  title: Our Clients love us!
  #  subtitle: Lorem ipsum sit dolor amet is a dummy text used by typography industry
  #  clients:
  #  - name: Irma Walters
  #    quote: Lorem ipsum dolor sit amet, elit deleniti dissentias quo eu, hinc minim appetere te usu, ea case duis scribentur has. Duo te consequat elaboraret, has quando suavitate at.
  #    job: Accountant
  #    img: 1
  #  - name: John Bradley
  #    quote: Lorem ipsum dolor sit amet, elit deleniti dissentias quo eu, hinc minim appetere te usu, ea case duis scribentur has. Duo te consequat elaboraret, has quando suavitate at.
  #    job: Financial Analyst
  #    img: 2
  #  - name: Gary Blackman
  #    quote: Lorem ipsum dolor sit amet, elit deleniti dissentias quo eu, hinc minim appetere te usu, ea case duis scribentur has. Duo te consequat elaboraret, has quando suavitate at.
  #    job: HR Manager
  #    img: 3
  # section5: true
  # section5 is a "contact us" form
  footer:
    # Logo (from /images/logos/___)
    logo: facile-white.svg
    # Social media links (GitHub, Twitter, etc.). All are optional.
    socialmedia:
    - link: https://github.com/facilebio
      # Icons are from Font Awesome
      icon: github
    - link: https://twitter.com/lianos_
      icon: twitter
    bulmalogo: true
    quicklinks:
      column1:
        title: "Documentation"
        links:
        - text: Getting Started
          link: /
        - text: The FacileData API
          link: /
        - text: RNA-seq analysis in the facileverse
          link: post/facile-rnaseq-analysis/
        - text: Roadmap
          link: /
      #column2:
      #  title: "Docs"
      #  links:
      #  - text: Get started
      #    link: /
      #  - text: The FacileData API
      #    link: /
      #  - text: Admin guide
      #    link: /
      #  - text: Developers
      #    link: /
      #column3:
      #  title: "Blog"
      #  links:
      #  - text: Latest news
      #    link: /blog/first
      #  - text: Tech articles
      #    link: /blog/second