Package index
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BRENDA - BRENDA tissue ontology obo file. using version 2021/10
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BRENDAExistName() - search for a valid BRENDA ontology term to use for sample type (deprecated 10/2025)
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OmicS_searchAssayType() - search for an assay type to use (deprecated 10/2025)
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OmicS_searchOrganism() - search for a pre-defined organism name to use (deprecated 10/2025)
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OmicS_searchPlatform() - search for a platform name to use (deprecated 10/2025)
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OmicS_searchSampleType() - OmicS_searchSampleType
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OmicSigFromDifexp() - create an OmicSignature object from differential expression matrix
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OmicSignature - OmicSignature R6 object
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OmicSignatureCollection - OmicSignatureCollection R6 object
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compare_label_pairing_example - Simulated signatures for label-pairing examples
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compare_mixed_direction_example - Simulated signatures mixing bi-directional and uni-directional signatures
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compare_omic_signatures() - Compare OmicSignature objects
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compare_signatures_example - Example signatures for comparing OmicSignature lists
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compare_unidirectional_example - Simulated signatures with only uni-directional signatures
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createMetadata() - template for creating a metadata list for an OmicSignature R6 object
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diffAnalLm() - differential expression analysis using limma package
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predefined_assaytypes - predefined assay type list
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predefined_organisms - predefined organism list
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predefined_platforms - predefined platform list
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readJson() - read an OmicSignature object from json txt file created by writeJson()
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replaceDifexpCol() - Standardize the column names of difexp
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signatureVecToDF() - change a signature vector into a dataframe to be saved into OmicSignature object
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signature_similarity_heatmap() - Plot signature similarity heatmaps
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standardizeSigDF() - Standardize signature data frame
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writeJson() - write OmicSignature object into json txt format