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_pkgdown.yml
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_pkgdown.yml
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url: https://omnideconv.github.io/omnideconv
reference:
- title: Main package methods
desc: Main methods to build signature matrices and deconvolute cell fractions.
contents:
- deconvolution_methods
- build_model
- deconvolute
- title: Signature matrix creation methods
desc: Direct access to the individual signature matrix creation methods.
contents:
- build_model_autogenes
- extract_signature_autogenes
- build_model_bayesprism
- build_model_bisque
- build_model_bseqsc
- build_model_cibersortx
- build_model_cpm
- build_model_dwls
- build_model_momf
- build_model_music
- build_model_scaden
- build_model_scdc
- title: Deconvolution methods
desc: Direct access to the individual deconvolution methods to access special features that are not available through `deconvolute`.
contents:
- deconvolute_autogenes
- deconvolute_bayesprism
- deconvolute_bisque
- deconvolute_bseqsc
- deconvolute_cibersortx
- deconvolute_cpm
- deconvolute_dwls
- deconvolute_momf
- deconvolute_music
- deconvolute_scaden
- deconvolute_scdc
- title: Environment
desc: Methods needed to set credentials or change variables in the environment.
contents:
- set_cibersortx_credentials
- bseqsc_config
- title: Datasets
desc: List of datasets provided by the package.
contents:
- bulk
- RefData
- cell_type_annotations_1
- cell_type_annotations_2
- cell_type_annotations_3
- single_cell_data_1
- single_cell_data_2
- single_cell_data_3
- batch_ids_1
- batch_ids_2
- batch_ids_3
- title: Visualisation
desc: Methods which produce plots with different methods.
contents:
- make_benchmarking_scatterplot
- make_barplot
- plot_deconvolution
- title: internal
contents:
- anndata_checkload
- anndata_is_identical
- anndata_to_singlecellexperiment
- autogenes_checkload
- build_anndata
- build_model_cdseq
- calculate_cell_embedding
- calc_condition_number
- check_and_install
- check_credentials
- convert_to_matrix
- create_container_command
- deconvolute_cdseq
- deescape_special_chars
- check_container
- setup_singularity_container
- escape_special_chars
- get_cell_fractions_options
- get_method_options
- get_signature_matrix_options
- get_single_cell_expression_set
- init_python
- install_all_python
- install_autogenes
- install_scaden
- matrix_to_singlecellexperiment
- normalize_deconv_results
- python_available
- read_anndata
- required_packages
- save_as_h5ad
- scaden_checkload
- scaden_predict
- scaden_process
- scaden_simulate
- scaden_simulate_example
- scaden_train
- sces_are_identical
- set_python
- singlecellexperiment_to_anndata
- singlecellexperiment_to_matrix
- transform_and_save_bulk
- transform_and_save_single_cell
- verbose_wrapper
- write_anndata