_pkgdown.yml

url: https://stuartlab.org/signac

home:
  links:
    - text: Contributors
      href: https://github.com/stuart-lab/signac/graphs/contributors
    - text: Roadmap
      href: https://github.com/orgs/stuart-lab/projects/1

navbar:
  title: "Signac"
  left:
    - text: "Install"
      href: articles/install.html
    - text: "News"
      href: news/index.html
    - text: "Get started"
      href: articles/overview.html
    - text: "FAQ"
      href: articles/faq.html
    - text: "Vignettes"
      menu:
        - text: "Vignettes overview"
          href: articles/overview.html
        - text: -------
        - text: "Human PBMCs"
          href: articles/pbmc_vignette.html
        - text: "Adult mouse brain"
          href: articles/mouse_brain_vignette.html
        - text: "Joint RNA and ATAC analysis: 10x multiomic"
          href: articles/pbmc_multiomic.html
        - text: "Joint RNA and ATAC analysis: SNARE-seq"
          href: articles/snareseq.html
        - text: "Peak calling"
          href: articles/peak_calling.html
        - text: "Merging objects"
          href: articles/merging.html
        - text: "scATAC-seq integration"
          href: articles/integrate_atac.html
        - text: "Mitochondrial genotyping"
          href: articles/mito.html
        - text: "Motif analysis"
          href: articles/motif_vignette.html
        - text: "Trajectory analysis"
          href: articles/monocle.html
        - text: "Finding co-accessible sites"
          href: articles/cicero.html
        - text: "Transcription factor footprinting"
          href: articles/footprint.html
        - text: "Data visualization"
          href: articles/visualization.html
        - text: "Parallel computing"
          href: articles/future.html
        - text: "Data structures and object interaction"
          href: articles/data_structures.html
    - text: "Reference"
      href: reference/index.html
    - text: "Archive"
      href: articles/archive.html
    - text: "Discussions"
      href: https://github.com/stuart-lab/signac/discussions
  right:
    - icon: fa-github
      href: https://github.com/stuart-lab/signac

reference:
  - title: "Object interaction"
    desc: "Functions for interacting with a Signac classes"
  - contents:
    - has_concept("assay")

  - title: "Quantification and peak calling"
    desc: "Functions for identifying and quantifying genomic regions"
  - contents:
    - has_concept("quantification")

  - title: "Preprocessing"
    desc: "Functions for preprocessing single-cell data"
  - contents:
    - has_concept("preprocessing")

  - title: "Quality control"
    desc: "Functions for performing quality control"
  - contents:
    - has_concept("qc")

  - title: "Dimension reduction"
    desc: "Functions for reducing dimensions"
  - contents:
    - has_concept("dimension_reduction")

  - title: "Visualization"
    desc: "Functions for visualizing single-cell data"
  - contents:
    - has_concept("visualization")

  - title: "Utilities"
    desc: "Utility functions for working with single-cell data"
  - contents:
    - has_concept("utilities")

  - title: "Footprinting"
    desc: "Functions for performing TF footprinting"
  - contents:
    - has_concept("footprinting")

  - title: "Motif analysis"
    desc: "Functions for performing DNA sequence motif analysis"
  - contents:
    - has_concept("motifs")

  - title: "Heatmaps"
    desc: "Functions for single-cell heatmaps"
  - contents:
    - has_concept("heatmap")

  - title: "Mitochondrial lineage tracing"
    desc: "Functions for identifying cell lineages or clonotypes from mitochondrial mutations"
  - contents:
    - has_concept("mito")

  - title: "Fragments"
    desc: "Functions for working with fragment files"
  - contents:
    - has_concept("fragments")

  - title: "Links"
    desc: "Functions for working with genomic links"
  - contents:
    - has_concept("links")

  - title: "Nearest methods"
    desc: "Nearest genomic range methods for Signac-defined classes"
  - contents:
    - has_concept("nearest")

  - title: "Inter-range methods"
    desc: "Inter-range methods for Signac-defined classes"
  - contents:
    - has_concept("inter_range")

  - title: "Overlap methods"
    desc: "Overlap-range methods for Signac-defined classes"
  - contents:
    - has_concept("overlaps")

  - title: "Coverage methods"
    desc: "Genomic range coverage methods for Signac-defined classes"
  - contents:
    - has_concept("coverage")

  - title: "Genomic range methods"
    desc: "Genomic ranges methods for Signac-defined classes"
  - contents:
    - has_concept("granges")

  - title: "Seqinfo methods"
    desc: "Seqinfo methods for Signac-defined classes"
  - contents:
    - has_concept("seqinfo")

  - title: "Data"
    desc: "Datasets included in Signac"
  - contents:
    - has_concept("data")
  
  - title: "internal"
  - contents:
    - has_concept("internal")

template:
  params:
    bootswatch: cosmo
    ganalytics: UA-144505535-1
    docsearch:
      api_key: 6f41d2052819b9deda704726769f8647
      index_name: signac