_pkgdown.yml

template:
  bootstrap: 5
  params:
    google_site_verification: GE78cdBqx5YPEbHjqtohe_p51Ng8oEPXdcaSEIu2dP8
url: https://kharchenkolab.github.io/numbat
home:
  title: Numbat Guide
  description: >
    Haplotype-aware CNV detection and phylogeny reconstruction from single-cell RNA-seq
footer:
  structure: 
    left: developed_by
reference:
- title: "Preparing data"
  contents: 
  - aggregate_counts
- title: "CNV detection"
  contents:
  - get_bulk
  - analyze_bulk
  - detect_clonal_loh
- title: "Single-cell clonal decomposition"
  contents:
  - run_numbat
- title: "Visualizing results"
  contents:
  - Numbat
  - get_gtree
  - starts_with("plot_")
  - cnv_heatmap
- title: "Example data"
  contents:
  - df_allele_example
  - count_mat_example
  - ref_hca
  - ref_hca_counts
  - bulk_example
  - annot_ref
  - count_mat_ref
  - gexp_roll_example
  - hc_example
  - joint_post_example
  - mut_graph_example
  - phylogeny_example
  - pre_likelihood_hmm
  - segs_example
- title: "Genome annotations"
  contents:
  - acen_hg19
  - acen_hg38
  - chrom_sizes_hg19
  - chrom_sizes_hg38
  - gaps_hg19
  - gaps_hg38
  - gtf_hg19
  - gtf_hg38
  - gtf_mm10
  - vcf_meta
- title: "Misc"
  contents:
  - annotate_genes
  - upgma
articles:
- title: "Tutorials"
  navbar: ~
  contents:
  - results
  - mouse
  - spatial-rna
  - descriptions