_pkgdown.yml

title: ArchR
url: https://www.ArchRProject.com
template:
  params:
    bootswatch: yeti
    ganalytics: UA-158769145-1
    docsearch:
      api_key: 252c2c36fedc32b3ed803d0db4877b96
      index_name: archr

authors:
  sidebar:
    roles: [aut, ctb]
  Jeffrey Granja:
    href: https://twitter.com/JeffreyGranja
  Ryan Corces:
    href: https://twitter.com/doctorcorces
  Paulina Paiz:
    href: https://twitter.com/paulinapaiz02
  Immanuel Abdi:
    href: https://github.com/immanuelazn

home:
  sidebar:
    structure: [links, license, community, authors, dev]

navbar:
  left:
  - icon: fa-home
    href: index.html
  - text: Quick Tutorial
    icon: fa-graduation-cap
    href: articles/Articles/tutorial.html
  - text: Full Manual
    icon: fa-file-text-o
    href: bookdown/index.html
  - text: Functions
    icon: fa-code
    href: reference/index.html
  right:
  - text: ArchR on GitHub
    icon: fa-github
    href: https://github.com/GreenleafLab/ArchR

toc:
  depth: 2

reference:
  - title: Arrow file creation
    desc: Functions that help create / set up an ArrowFile
    contents:
    - createArrowFiles
    - createGeneAnnotation
    - createGenomeAnnotation
    - filterDoublets
    - nCells
    - reformatFragmentFiles
    - setArchRLocking
  - title: Add-ers
    desc: Functions that add information to ArrowFiles or an ArchRProject
    contents:
    - starts_with("add")
  - title: Get-ers
    desc: Functions that get information from ArrowFiles or an ArchRProject
    contents:
    - starts_with("get")
  - title: Manipulating an ArchRProject
    desc: Functions for manipulating an ArchRProject
    contents:
    - ArchRProject
    - loadArchRProject
    - recoverArchRProject
    - saveArchRProject
    - subsetArchRProject
    - subsetCells
  - title: Plotting / aesthetic functions
    desc: Functions for plotting in ArchR
    contents:
    - ArchRBrowser
    - ArchRHeatmap
    - ArchRPalettes
    - starts_with("gg")
    - starts_with("palette")
    - starts_with("plot")
    - starts_with("theme")
  - title: Helper functions
    desc: Functions that make things easier
    contents:
    - '%ni%'
    - '%bcin%'
    - '%bcni%'
    - createLogFile
    - findMacs2
    - installExtraPackages
    - validBSgenome
  - title: GRanges manipulation
    desc: Functions to manipulate GRanges objects
    contents:
    - extendGR
    - filterChrGR
    - nonOverlappingGR
  - title: Multiome functions
    desc: Functions specifically related to handling multiomic data
    contents:
    - import10xFeatureMatrix
  - title: Other ArchR Functions
    desc: Functions that didnt fit into one of the above categories
    contents:
    - confusionMatrix
    - correlateMatrices
    - correlateTrajectories
    - customEnrichment
    - exportPeakMatrixForSTREAM
    - imputeMatrix
    - mapLabels
    - peakAnnoEnrichment
    - projectBulkATAC
  - title: internal
    desc: Internal functions not to be displayed on the ref page
    contents:
    - $.ArchRProject
    - $<-.ArchRProject
    - .DollarNames.ArchRProject
    - matches("\\[.ArchRProject")
    - .suppressSpecificWarnings