Function reference • omnideconv

Main package methods Main methods to build signature matrices and deconvolute cell fractions.
`deconvolution_methods`	List of supported deconvolution methods
`build_model()`	Building the signature matrix
`deconvolute()`	Deconvolution
Signature matrix creation methods Direct access to the individual signature matrix creation methods.
`build_model_autogenes()`	Calculates the signature model with AutoGeneS
`extract_signature_autogenes()`	Extraction of the signature matrix from autogenes .pickle files
`build_model_bayesprism()`	No model is built as BayesPrism performs signature building and deconvolution in one step.
`build_model_bisque()`	No model is build as Bisque does both steps in one.
`build_model_bseqsc()`	Calculates the signature model with BSeq-sc
`build_model_cibersortx()`	Signature matrix creation with CIBERSORTx
`build_model_cpm()`	No model is build as CPM does not use a signature matrix.
`build_model_dwls()`	Signature matrix creation with DWLS using genes identified by a differential analysis
`build_model_momf()`	Calculates the signature model with MOMF
`build_model_music()`	Signature creation with MuSiC.
`build_model_scaden()`	Builds Scaden Model from scRNA data
`build_model_scdc()`	Signature creation with SCDC.
Deconvolution methods Direct access to the individual deconvolution methods to access special features that are not available through `deconvolute`.
`deconvolute_autogenes()`	Deconvolution Analysis using AutoGeneS
`deconvolute_bayesprism()`	Bayesian deconvolution module using BayesPrism
`deconvolute_bisque()`	Calculates the decomposition using the bisque algorithm IMPORTANT: No model is needed. Everything is done inside this method.
`deconvolute_bseqsc()`	Deconvolution Analysis using BSeq-sc
`deconvolute_cibersortx()`	Deconvolute with CIBERSORTx
`deconvolute_cpm()`	CPM Deconvolution
`deconvolute_dwls()`	Calculates the decomposition using the dwls algorithm
`deconvolute_momf()`	Deconvolution Analysis using MOMF (via Nonnegative Factorization)
`deconvolute_music()`	MuSiC Deconvolution
`deconvolute_scaden()`	Performs deconvolution with Scaden
`deconvolute_scdc()`	SCDC Deconvolution
Environment Methods needed to set credentials or change variables in the environment.
`set_cibersortx_credentials()`	Setting the CIBERSORTx Credentials
`bseqsc_config()`	Setup BSeq-SC External Dependencies
Datasets List of datasets provided by the package.
`bulk`	Example RNA-seq dataset from Hoek et al.
`RefData`	Gold standard measurements with FACS from Hoek et al.
`cell_type_annotations_1`	Cell Type Annotations Number 1 from Hao et al.
`cell_type_annotations_2`	Cell Type Annotations Number 2 from Hao et al.
`cell_type_annotations_3`	Cell Type Annotations Number 3 from Hao et al.
`single_cell_data_1`	Example single-cell RNA-seq dataset Number 1 from Hao et al.
`single_cell_data_2`	Example single-cell RNA-seq dataset Number 2 from Hao et al.
`single_cell_data_3`	Example single-cell RNA-seq dataset Number 3 from Hao et al.
`batch_ids_1`	Patient ids Number 1 from Hao et al.
`batch_ids_2`	Patient ids Number 2 from Hao et al.
`batch_ids_3`	Patient ids Number 3 from Hao et al.
Visualisation Methods which produce plots with different methods.
`make_benchmarking_scatterplot()`	Make a Scatterplot for Benchmarking
`make_barplot()`	Plot deconvolution results as a barplot
`plot_deconvolution()`	Plot Deconvolution results

Reference

Main package methods

Signature matrix creation methods

Deconvolution methods

Environment

Datasets

Visualisation