Reference

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. This function can be used in case that the signature should be examined. The final signature is stored as a pickle file.
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. One-step function that performs signature building and deconvolution in one step without saving the signature in between. A signature that has been created with @seealso build_model_autogenes() can be supplied as input to this function with the signature parameter, although it is not mandatory.
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
check_container()	Checks wether docker/apptainer are available and can be used
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