_pkgdown.yml

url: https://http://josephng-bio.org/sciCSR
template:
  bootstrap: 5
  bootswatch: yeti
  bslib:
    pkgdown-nav-height: 100px
    primary: "#0d0e0f"
    code-bg: "#bfcadb"
figures:
   dev: grDevices::png
pkgdown:
  as_is: true
navbar:
  structure:
    left:  [intro, reference, articles, tutorials, news]
    right: [mysite, search, github, twitter]
  components:
    mysite:
      text: Joseph Ng's website
      href: https://josephng-bio.org
    twitter:
      icon: fa-twitter
      href: https://twitter.com/JosefNg1
      aria-label: Twitter
    github:
      icon: fa-github
      href: https://github.com/Fraternalilab/sciCSR/
      aria-label: github
articles:
- title: Analysing Class-Switch Recombination in B cell scRNA-seq data using sciCSR
  navbar: Basic sciCSR usage
  contents:
  - csr
- title: Comparing state transitions inferred using CSR, SHM and RNA velocity
  navbar: Comparing CSR/SHM/RNA velocity
  contents:
  - comparison
reference:
- title: "Setting up dependencies"
  desc: "Wrapper to set up python dependencies."
  contents:
  - prepare_sciCSR
- title: "scRNA-seq data processing and wrangling"
  desc: "Functions for basic scRNA-seq data processing wrangling, including B-cell-specific functionalities."
  contents:
  - collapseIntoMetagenes
  - normalise_dimreduce
  - guessBarcodes
  - repairBarcode
  - convertSeuratToH5ad
  - splitAnnData
  - read_loom_matrices
  - combineLoomFiles
- title: "Merging Repertoire and scRNA-seq read counts"
  desc: "Functions for additing repertoire annotation features as metadata to gene expression count matrices."
  contents:
  - annotatePairing
  - collapseBCR
  - AddCellMetaToVDJ
  - combineBCR
- title: "CSR/SHM-based pseudotime"
  desc: "Functions for extracting and calculating cell pseudotime ordering using CSR and SHM information."
  contents:
  - scanBam
  - getIGHmapping
  - getIGHreadType
  - getJunctionReads
  - summariseIGHreads
  - mergeIgHCountsToSeurat
  - getCSRpotential
  - getSHM
  - getIsotype
- title: "RNA velocity"
  desc: "RNA velocity analysis in R by interfacing with python packages"
  contents:
  - mergeVelocytoWithGEX
  - run_scVelo
- title: "Inferring transitions"
  desc: "Inferring transitions using CSR/SHM information or RNA velocity"
  contents:
  - fitTransitionModel
  - fitTPT
  - compareTransitionMatrices
- title: "Data visualisation"
  desc: "Visualising inferred transitions"
  contents:
  - starts_with("plot")
- title: "Data objects"
  desc: "Data objects underlying sciCSR functionalities"
  contents:
  - starts_with("human")
  - starts_with("mouse")