Package index
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handle_duplicates()
- Handle duplicate identifiers in an expression matrix
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extract_identifiers()
- Extract primary identifiers from e.g. protein groups
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update_gene_symbols()
- Update gene symbols in a matrix to approved HGNC nomenclature
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unlog2_data()
- Convert data from log2 scale to linear scale
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convert_to_tpm()
- Convert protein abundance data to TPM-like normalization
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handle_scaling()
- Handle scaling of protein abundance data
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handle_missing_values()
- Handle missing values
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map_cell_groups()
- Map column names to cell type groups using patterns
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create_phenoclasses()
- Create phenoclasses matrix for cell type deconvolution
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create_signature_matrix()
- Create signature matrix using CIBERSORTx
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deconvolute()
- Deconvolute protein data using multiple algorithms
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deconvolute_bayesdebulk()
- Deconvolute bulk proteome data using BayesDeBulk
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deconvolute_cibersort()
- Deconvolute mixture data using CIBERSORT
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deconvolute_cibersortx()
- Deconvolute using CIBERSORTx Docker image
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deconvolute_epic()
- Deconvolute bulk data using EPIC
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simulate_data()
- Simulate artifical mixtures from bulk proteome measurements