Package index
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Annotation - Class representing annotation for expression data.
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DOWN_COLOR - Color palette for nexomis: Down blue
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ExprData - An R6 class representing an RNA-Seq expression dataset.
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ExprDataGene - Class representing an expression dataset at gene-level
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ExprDataTranscript - Class representing an expression dataset at transcript-level
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MID_COLOR - Color palette for nexomis: Mid yellow-white
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NA_COLOR - Color palette for nexomis: Down blue
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PairwiseComp - Generate Crossed Lists from Nested Results
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PairwiseDESeq2 - DESeq2 Results from Pairwise Design
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PairwiseDearseq - Dearseq Results from Pairwise Design
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PairwiseDesign - Class representing metadata for expression data: Design
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PairwiseLFC - Class representing raw Log Fold change results from a pairwaise design
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RStanAnalysis - Class runing the bayesian model for the distribution parameters inference
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THEME_NEXOMIS - ggplot2 theme for nexomis
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UP_COLOR - Color palette for nexomis: Up red
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UP_TO_DOWN_GRADIENT_COLORS - Color palette gradient for nexomis from UP red to DOWN blue through MID yellow-white
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create_uniprot_gene_id_mappings() - utils function for this class only scores min given for unique first and then for dups before merging switch to data.table
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fetch_id_mapping() - Extract id_mapping table from UniProt API
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geom_mean_modified() - Modified geometric mean function
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make_test_data() - Simulate data from config
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parse_gff_to_annotation() - Parse GFF file to annotation format
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plot_summarized_etags() - Helper function for ExprData$sum_per_type_per_sample
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remove_id_version_suffix() - Remove version suffixes from a vector of IDs
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safe_translate_ids() - Safely translate IDs using a named vector
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simple_chord() - Generate a simple chord plot