_pkgdown.yml

url: https://icbi-lab.github.io/immunedeconv

reference:
  - title: Deconvolution
    desc: Use the package to estimate immune cell fractions from bulk RNA-seq samples.
    contents:
      - deconvolution_methods
      - deconvolute
      - set_cibersort_binary
      - set_cibersort_mat
      - eset_to_matrix
  - title: Deconvolution methods
    desc: Direct access to the individual deconvolution methods to access special features that are not available through `deconvolute()`.
    contents:
      - deconvolute_cibersort
      - deconvolute_epic
      - deconvolute_mcp_counter
      - deconvolute_quantiseq
      - deconvolute_timer
      - deconvolute_xcell
  - title: Cell type mapping
    desc: Map cell types and datasets to a controlled vocabulary.
    contents:
      - cell_type_map
      - cell_type_tree
      - available_datasets
      - map_cell_types
      - map_result_to_celltypes
  - title: Simulation of bulk samples
    desc: Use this package to simulate bulk RNA-seq samples from single cell RNA-seq data.
    contents:
      - scale_to_million
      - make_random_bulk
      - make_bulk_eset
  - title: Datasets
    desc: List of datasets provided by the package
    contents:
      - dataset_racle
  - title: TIMER
    desc: functions and objects related to the TIMER method
    contents:
      - timer_available_cancers
      - deconvolute_timer
  - title: quanTIseq
    desc: functions and objects related to the quanTIseq method
    contents:
     - deconvolute_quantiseq.default