echoannot/_pkgdown.yml at main · RajLabMSSM/echoannot · GitHub

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url: https://rajlabmssm.github.io/echoannot/

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navbar:
  structure:
    left: [intro, reference, articles, news]
    right: [search, github]
  components:
    github:
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      href: https://github.com/RajLabMSSM/echoannot

articles:
  - title: Getting started
    contents:
      - echoannot
  - title: Epigenomics
    contents:
      - cell_type_specific_epigenomics

reference:
  - title: Annotation functions
    desc: Annotate SNPs with functional information
    contents:
      - annotate_snps
      - annotate_missense
      - annotation_file_name
  - title: NOTT2019 data
    desc: Brain cell-type-specific epigenomic data from Nott et al. 2019
    contents:
      - NOTT2019_epigenomic_histograms
      - NOTT2019_get_epigenomic_peaks
      - NOTT2019_get_interactome
      - NOTT2019_get_promoter_interactome_data
      - NOTT2019_get_regulatory_regions
      - NOTT2019_plac_seq_plot
      - get_NOTT2019_superenhancer_interactome
  - title: CORCES2020 data
    desc: Single-cell epigenomic data from Corces et al. 2020
    contents:
      - CORCES2020_get_ATAC_peak_overlap
      - CORCES2020_get_hichip_fithichip_overlap
      - get_CORCES2020_bulkATACseq_peaks
      - get_CORCES2020_cicero_coaccessibility
      - get_CORCES2020_hichip_fithichip_loop_calls
      - get_CORCES2020_scATACseq_celltype_peaks
      - get_CORCES2020_scATACseq_peaks
  - title: GOSHIFTER
    desc: GoShifter enrichment analysis
    contents:
      - GOSHIFTER
      - GOSHIFTER_run
      - GOSHIFTER_heatmap
      - GOSHIFTER_histograms_SNPgroups
      - GOSHIFTER_histograms_pvals
  - title: MOTIFBREAKR
    desc: Motif disruption analysis
    contents:
      - MOTIFBREAKR
      - MOTIFBREAKR_calc_pvals
      - MOTIFBREAKR_filter
      - MOTIFBREAKR_plot
      - MOTIFBREAKR_summarize
  - title: XGR
    desc: Genomic region annotation via XGR
    contents:
      - XGR_enrichment
      - XGR_filter_assays
      - XGR_filter_sources
      - XGR_query
  - title: ROADMAP
    desc: Roadmap Epigenomics chromatin state annotations
    contents:
      - ROADMAP_construct_reference
      - ROADMAP_query
  - title: Plotting
    desc: Summary and visualization functions
    contents:
      - CS_bin_plot
      - CS_counts_plot
      - super_summary_plot
      - peak_overlap_plot
      - plot_dataset_overlap
      - plot_missense
      - convert_plots
      - merge_celltype_specific_epigenomics
  - title: Utilities
    desc: Helper functions
    contents:
      - add_mb
      - granges_overlap
      - get_window_limits
      - import_ucsc_bigwigs
      - test_enrichment
      - annotation_file_name
  - title: Bundled data
    contents:
      - NOTT2019_bigwig_metadata
      - xgr_example
      - XGR_enrichment_bootstrap