Deconvolution

Use the package to estimate immune cell fractions from bulk RNA-seq samples.

deconvolution_methods

List of supported immune deconvolution methods

deconvolute()

Perform an immune cell deconvolution on a dataset.

set_cibersort_binary()

Set Path to CIBERSORT R script (CIBERSORT.R)

set_cibersort_mat()

Set Path to CIBERSORT matrix file (LM22.txt)

eset_to_matrix()

Convert a Biobase::ExpressionSet to a gene-expression matrix.

Deconvolution for mouse data

Use the package to estimate immune cell fractions from murine bulk RNA-seq samples.

deconvolution_methods_mouse

List of supported mouse deconvolution methods The methods currently supported are mmcp_counter, seqimmucc, dcq, base The object is a named vector. The names correspond to the display name of the method, the values to the internal name.

deconvolute_mouse()

Perform deconvolution on a mouse RNAseq dataset

Deconvolution methods

Direct access to the individual deconvolution methods to access special features that are not available through deconvolute().

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_timer()

Deconvolute using TIMER

deconvolute_xcell()

Deconvolute using xCell

deconvolute_abis()

Deconvolute using ABIS.

deconvolute_consensus_tme()

Deconvolute using ConsensusTME.

deconvolute_estimate()

Source code for the ESTIMATE algorithm: Estimate of Stromal and Immune Cells in Malignant Tumor Tissues from Expression Data (https://doi.org/10.1038/ncomms3612) Source: http://r-forge.r-project.org/projects/estimate/ Copyright: 2013-2022, MD Anderson Cancer Center (MDACC) License: GPL-2

Deconvolution methods for mouse data

Direct access to the individual mouse deconvolution methods to access special features that are not available through deconvolute().

deconvolute_mmcp_counter()

Deconvolute using mMCP-counter

deconvolute_seqimmucc()

Deconvolute using seqImmuCC

deconvolute_base_algorithm()

Deconvolute using BASE

deconvolute_dcq()

Deconvolute using DCQ

convert_human_mouse_genes()

This function converts the mouse gene symbols into corresponding human ones, and vice versa.

Deconvolution methods with custom signature

Access to the individual deconvolution methods that allow the use of a custom signature (matrix or gene set)

custom_deconvolution_methods

List of methods that support the use of a custom signature

deconvolute_cibersort_custom()

Deconvolute using CIBERSORT or CIBERSORT abs and a custom signature matrix.

deconvolute_epic_custom()

Deconvolute using EPIC and a custom signature matrix.

deconvolute_base_custom()

Deconvolute using BASE and a custom signature matrix

deconvolute_consensus_tme_custom()

Deconvolute using ConsesnusTME and a custom signature matrix

Cell type mapping

Map cell types and datasets to a controlled vocabulary.

cell_type_map

Table mapping the cell types from methods/datasets to a single, controlled vocabulary.

cell_type_tree

Available cell types in the controlled vocabulary organized as a lineage tree.

available_datasets

Available methods and datasets.

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.

get_dcq_cell_types_list()

This function returns the list of all cell types in BASE/DCQ results, along with the cell type they are mapped to

reduce_mouse_cell_types()

Since DCQ and BASE provide estimates for several cell types, this function combines the results to align them with the rest of the methods

Simulation of bulk samples

Use this package to simulate bulk RNA-seq samples from single cell RNA-seq data.

scale_to_million()

Scale sample to TPM

make_random_bulk()

Make a random bulk sample from a single-cell dataset

make_bulk_eset()

Make a random expression set from a single-cell dataset

Datasets

List of datasets provided by the package

dataset_racle

Example RNA-seq dataset from the EPIC publication.

dataset_petitprez

Example RNA-seq dataset from the mMCP_Counter publication.

TIMER

functions and objects related to the TIMER method

timer_available_cancers

TIMER signatures are cancer specific. This is the list of available cancer types.

deconvolute_timer()

Deconvolute using TIMER