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| .get_all_children | Recursive helper function for get_all_children. |
| annotate_cell_type | Annotate unified cell_type names |
| available_datasets | Available methods and datasets. |
| cell_type_list | List with controlled cell-type vocabulary |
| cell_type_map | Table mapping the cell types from methods/datasets to a single, controlled vocabulary. |
| cell_type_mapping | Functions for mapping cell types between deconvolution methods and datasets. |
| cell_type_tree | Available cell types in the controlled vocabulary organized as a lineage tree. |
| check_cancer_types | process batch table and check cancer types. |
| dataset_racle | Example RNA-seq dataset from the EPIC publication. |
| deconvolute | Perform an immune cell deconvolution on a dataset. |
| deconvolute_cibersort | Deconvolute using CIBERSORT or CIBERSORT abs. |
| deconvolute_epic | Deconvolute using EPIC |
| deconvolute_mcp_counter | Deconvolute using MCP-counter |
| deconvolute_quantiseq | Deconvolute using quanTIseq |
| deconvolute_quantiseq.default | Use quanTIseq to deconvolute a gene expression matrix. |
| deconvolute_timer | Deconvolute using TIMER |
| deconvolute_xcell | Deconvolute using xCell |
| deconvolution_methods | List of supported immune deconvolution methods |
| eset_to_matrix | Convert a 'Biobase::ExpressionSet' to a gene-expression matrix. |
| find_children | Recursive helper function for map_cell_types. |
| fix_namespace | assign the following global variables .onLoad because of 'staged-install' |
| GetFractions.Abbas | Constrained regression method implemented in Abbas et al., 2009 |
| get_all_children | Get all children of a certain cell type. |
| immunedeconv | Collection of immune cell deconvolution methods. |
| make_bulk_eset | Make a random expression set from a single-cell dataset |
| make_random_bulk | Make a random bulk sample from a single-cell dataset |
| map_cell_types | Use a tree-hierarchy to map cell types among different methods. |
| map_result_to_celltypes | Map a result table as generated by 'deconvolute' to a user-defined list of cell types. |
| node_by_name | Lookup dictionary for cell-type nodes |
| quantiseq_helper | Helper functions for quanTIseq |
| scale_to_million | Scale sample to TPM |
| set_cibersort_binary | Set Path to CIBERSORT R script ('CIBERSORT.R') |
| set_cibersort_mat | Set Path to CIBERSORT matrix file ('LM22.txt') |
| single_cell_simulation | Functions for generating simulated bulk samples from a single cell dataset. |
| summarise_children | sum up the fraction of all child nodes to a single value. Take into account which cell types are optional. |
| timer | Source code for the TIMER deconvolution method. |
| timer_available_cancers | TIMER signatures are cancer specific. This is the list of available cancer types. |
| xCell.data | Data object from xCell. |