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Data preprocessing

Functions for handling and processing protein data.

handle_duplicates()
Handle duplicate identifiers in an expression matrix
extract_identifiers()
Extract primary identifiers from e.g. protein groups
update_gene_symbols()
Update gene symbols in a matrix to approved HGNC nomenclature
unlog2_data()
Convert data from log2 scale to linear scale
convert_to_tpm()
Convert protein abundance data to TPM-like normalization
handle_scaling()
Handle scaling of protein abundance data
handle_missing_values()
Handle missing values

Signature matrix creation

Functions for working with signature matrix creation.

map_cell_groups()
Map column names to cell type groups using patterns
create_phenoclasses()
Create phenoclasses matrix for cell type deconvolution
create_signature_matrix()
Create signature matrix using CIBERSORTx

Deconvolution

Functions for deconvoluting bulk data into cell type proportions.

deconvolute()
Deconvolute protein data using multiple algorithms
deconvolute_bayesdebulk()
Deconvolute bulk proteome data using BayesDeBulk
deconvolute_cibersort()
Deconvolute mixture data using CIBERSORT
deconvolute_cibersortx()
Deconvolute using CIBERSORTx Docker image
deconvolute_epic()
Deconvolute bulk data using EPIC

Simulation

Function for simulating artifical mixtures.

simulate_data()
Simulate artifical mixtures from bulk proteome measurements