X_cibersort             Cibersort reference
adjust_abundance        Adjust transcript abundance for unwanted
                        variation
aggregate_duplicates    Aggregates multiple counts from the same
                        samples (e.g., from isoforms), concatenates
                        other character columns, and averages other
                        numeric columns
as_SummarizedExperiment
                        as_SummarizedExperiment
as_matrix               Get matrix from tibble
cluster_elements        Get clusters of elements (e.g., samples or
                        transcripts)
deconvolve_cellularity
                        Get cell type proportions from samples
describe_transcript     Get DESCRIPTION from gene SYMBOL for Human and
                        Mouse
fill_missing_abundance
                        Fill transcript abundance if missing from
                        sample-transcript pairs
get_X_cibersort         Get Cibersort reference data
get_bibliography        Produces the bibliography list of your workflow
identify_abundant       Identify abundant transcripts/genes
impute_missing_abundance
                        impute transcript abundance if missing from
                        sample-transcript pairs
keep_abundant           Filter to keep only abundant transcripts/genes
keep_abundant,RangedSummarizedExperiment-method
                        keep_abundant
keep_abundant,SummarizedExperiment-method
                        keep_abundant
keep_variable           Keep variable transcripts
log10_reverse_trans     Log10 reverse transformation for ggplot2
logit_trans             logit scale
pivot_sample            Extract sample-wise information
pivot_transcript        Extract transcript-wise information
quantile_normalise_abundance
                        Normalise by quantiles the counts of
                        transcripts/genes
reduce_dimensions       Dimension reduction of the transcript abundance
                        data
remove_redundancy       Drop redundant elements (e.g., samples) for
                        which feature (e.g., transcript/gene)
                        abundances are correlated
resolve_complete_confounders_of_non_interest
                        Resolve Complete Confounders of Non-Interest
resolve_complete_confounders_of_non_interest,SummarizedExperiment-method
                        resolve_complete_confounders_of_non_interest
rotate_dimensions       Rotate two dimensions (e.g., principal
                        components) of an arbitrary angle
scale_abundance         Scale the counts of transcripts/genes
scale_x_log10_reverse   scale_x_log10_reverse
scale_y_log10_reverse   scale_y_log10_reverse
test_differential_abundance
                        Perform differential transcription testing
                        using edgeR quasi-likelihood (QLT), edgeR
                        likelihood-ratio (LR), limma-voom,
                        limma-voom-with-quality-weights or DESeq2
test_differential_expression
                        Perform differential expression testing using
                        edgeR quasi-likelihood (QLT), edgeR
                        likelihood-ratio (LR), limma-voom,
                        limma-voom-with-quality-weights or DESeq2
test_gene_enrichment    analyse gene enrichment with EGSEA
test_gene_overrepresentation
                        analyse gene over-representation with GSEA
test_gene_rank          analyse gene rank with GSEA
test_stratification_cellularity,SummarizedExperiment-method
                        test_stratification_cellularity
tximeta_summarizeToGene_object
                        Needed for tests
                        tximeta_summarizeToGene_object, It is
                        SummarizedExperiment from tximeta
vignette_manuscript_signature_boxplot
                        Needed for vignette
                        vignette_manuscript_signature_boxplot
vignette_manuscript_signature_tsne
                        Needed for vignette
                        vignette_manuscript_signature_tsne
vignette_manuscript_signature_tsne2
                        Needed for vignette
                        vignette_manuscript_signature_tsne2
