_pkgdown.yml

title: metabaR
url: https://metabarfactory.github.io/metabaR/
development:
  mode: auto

reference:
  - title: Import / Format
    desc: Generate `metabarlist objects` from files of various formats or directly from R objects
    contents:
      - '`tabfiles_to_metabarlist`'
      - '`obifiles_to_metabarlist`'
      - '`biomfiles_to_metabarlist`'
      - '`read_ngsfilter`'
      - '`metabarlist_generator`'
      - '`check_metabarlist`'
      - '`silva_annotator`'
      - '`silva_annotator_deprec`'

  - title: Visualise
    desc: Visualise data under both ecological and experimental perspectives
    contents:
      - '`summary_metabarlist`'
      - '`ggpcrplate`'
      - '`ggpcrtag`'
      - '`ggtaxplot`'
      - '`hill_rarefaction`'
      - '`gghill_rarefaction`'
      - '`check_pcr_repl`'
      - '`check_pcr_thresh`'

  - title: Manipulate
    desc: Manipulate `metabarlist` objects
    contents:
      - '`subset_metabarlist`'
      - '`extract_table`'
      - '`aggregate_pcrs`'
      - '`aggregate_motus`'
      - '`taxoparser`'
      - '`taxodecider`'

  - title: Flag spurious signal
    desc: Detect and enable the tagging of potential molecular artifacts such as contaminants or failed PCR reactions
    contents:
      - '`contaslayer`'
      - '`tagjumpslayer`'
      - '`pcrslayer`'
      - '`pcr_outlier`'
      - '`pcr_within_between`'

  - title: Export
    desc: Export data in fasta format
    contents:
      - '`fasta_generator`'

  - title: Example data set
    contents:
      - '`soil_euk`'