Man pages for grst/immunedeconv
Methods for immune cell deconvolution
| annotate_cell_type | Annotate unified cell_type names |
| available_datasets | Available methods and datasets. |
| base_algorithm | Souce code for the BASE algorithm. This code is adapted from... |
| cell_type_list | List with controlled cell-type vocabulary |
| cell_type_map | Table mapping the cell types from methods/datasets to a... |
| cell_type_mapping | Functions for mapping cell types between deconvolution... |
| cell_type_tree | Available cell types in the controlled vocabulary organized... |
| check_cancer_types | process batch table and check cancer types. |
| convert_human_mouse_genes | This function converts the mouse gene symbols into... |
| create_base_compendium | Souce code to create the compendium used kin the BASE... |
| custom_deconvolution | Collection of deconvolution methods that allow custom... |
| custom_deconvolution_methods | List of methods that support the use of a custom signature |
| dataset_petitprez | Example RNA-seq dataset from the mMCP_Counter publication. |
| dataset_racle | Example RNA-seq dataset from the EPIC publication. |
| deconvolute | Perform an immune cell deconvolution on a dataset. |
| deconvolute_abis | Deconvolute using ABIS. |
| deconvolute_abis_default | Use ABIS to deconvolute a gene expression matrix. |
| deconvolute_base_algorithm | Deconvolute using BASE |
| deconvolute_base_custom | Deconvolute using BASE and a custom signature matrix |
| deconvolute_cibersort | Deconvolute using CIBERSORT or CIBERSORT abs. |
| deconvolute_cibersort_custom | Deconvolute using CIBERSORT or CIBERSORT abs and a custom... |
| deconvolute_consensus_tme | Deconvolute using ConsensusTME. |
| deconvolute_consensus_tme_custom | Deconvolute using ConsesnusTME and a custom signature matrix |
| deconvolute_dcq | Deconvolute using DCQ |
| deconvolute_epic | Deconvolute using EPIC |
| deconvolute_epic_custom | Deconvolute using EPIC and a custom signature matrix. |
| deconvolute_estimate | Source code for the ESTIMATE algorithm: Estimate of Stromal... |
| deconvolute_mcp_counter | Deconvolute using MCP-counter |
| deconvolute_mmcp_counter | Deconvolute using mMCP-counter |
| deconvolute_mouse | Perform deconvolution on a mouse RNAseq dataset |
| deconvolute_quantiseq | Deconvolute using quanTIseq |
| deconvolute_seqimmucc | Deconvolute using seqImmuCC |
| deconvolute_timer | Deconvolute using TIMER |
| deconvolute_xcell | Deconvolute using xCell |
| deconvolution_methods | List of supported immune deconvolution methods |
| deconvolution_methods_mouse | List of supported mouse deconvolution methods The methods... |
| dot-get_all_children | Recursive helper function for get_all_children. |
| eset_to_matrix | Convert a 'Biobase::ExpressionSet' to a gene-expression... |
| find_children | Recursive helper function for map_cell_types. |
| fix_namespace | assign the following global variables .onLoad because of... |
| get_all_children | Get all children of a certain cell type. |
| get_dcq_cell_types_list | This function returns the list of all cell types in BASE/DCQ... |
| GetFractions.Abbas | Constrained regression method implemented in Abbas et al.,... |
| 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... |
| map_result_to_celltypes | Map a result table as generated by 'deconvolute' to a... |
| mouse_cell_type_mapping | Functions for mapping cell types between deconvolution... |
| mouse_deconvolution | Collection of deconvolution methods for mouse data. |
| node_by_name | Lookup dictionary for cell-type nodes |
| reduce_mouse_cell_types | Since DCQ and BASE provide estimates for several cell types,... |
| scale_to_million | Scale sample to TPM |
| seqImmuCC_LLSR | Source code for the Linear Least Square Regression performed... |
| 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... |
| summarise_children | sum up the fraction of all child nodes to a single value.... |
| timer | Source code for the TIMER deconvolution method. |
| timer_available_cancers | TIMER signatures are cancer specific. This is the list of... |
| xCell.data | Data object from xCell. |
