Package index

Core workflows

run_expranno()

Run the full expranno workflow

annotate_expr()

Annotate an expression matrix

benchmark_annotation_engines()

Benchmark annotation engines on the same input

validate_annotation_engines()

Validate annotation engines against a truth table

merge_expr_meta()

Merge annotated expression and metadata

run_cell_deconvolution()

Run immune deconvolution

run_signature_analysis()

Run GSVA or ssGSEA signature scoring

Input and output helpers

as_expranno_input()

Coerce Bioconductor containers to expranno inputs

as_expranno_se()

Convert expranno output to SummarizedExperiment

list_annotation_presets()

List built-in annotation presets

example_annotation_truth()

Example annotation truth tables

validate_expr()

Validate an expression table

validate_meta()

Validate a metadata table

read_genesets()

Read gene sets from a GMT file

example_expranno_data()

Example expression and metadata inputs