_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 for mouse data
    desc: Use the package to estimate immune cell fractions from murine bulk RNA-seq samples.
    contents:
      - deconvolution_methods_mouse
      - deconvolute_mouse
  - 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
      - deconvolute_abis
      - deconvolute_consensus_tme
      - deconvolute_estimate
  - title: Deconvolution methods for mouse data
    desc: Direct access to the individual mouse deconvolution methods to access special features that are not available through `deconvolute()`.
    contents:
      - deconvolute_mmcp_counter
      - deconvolute_seqimmucc
      - deconvolute_base_algorithm
      - deconvolute_dcq
      - mouse_genes_to_human
  - title: Deconvolution methods with custom signature
    desc: Access to the individual deconvolution methods that allow the use of a custom signature (matrix or gene set)
    contents:
      - custom_deconvolution_methods
      - deconvolute_cibersort_custom
      - deconvolute_epic_custom
      - deconvolute_base_custom
      - deconvolute_consensus_tme_custom
  - 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
      - get_dcq_cell_types_list
      - reduce_mouse_cell_types
  - 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
      - dataset_petitprez
  - 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
  - title: internal
    contents:
      - xCell.data
      - timer
      - annotate_cell_type
      - cell_type_list
      - cell_type_mapping
      - check_cancer_types
      - .get_all_children
      - find_children
      - GetFractions.Abbas
      - fix_namespace
      - single_cell_simulation
      - get_all_children
      - immunedeconv
      - node_by_name
      - quantiseq_helper
      - summarise_children
      - deconvolute_abis_default
      - seqImmuCC_LLSR
      - base_algorithm
      - create_base_compendium
      - mouse_deconvolution
      - mouse_cell_type_mapping
      - custom_deconvolution