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
arrange                 Arrange rows by column values
as_SummarizedExperiment
                        as_SummarizedExperiment
as_matrix               Get matrix from tibble
bind_cols               Left join datasets
bind_rows               Efficiently bind multiple data frames by row
                        and column
breast_tcga_mini_SE     Needed for vignette breast_tcga_mini_SE
cluster_elements        Get clusters of elements (e.g., samples or
                        transcripts)
counts_ensembl          Counts with ensembl annotation
deconvolve_cellularity
                        Get cell type proportions from samples
describe_transcript     Get DESCRIPTION from gene SYMBOL for Human and
                        Mouse
distinct                distinct
ensembl_symbol_mapping
                        Data set
ensembl_to_symbol       Add transcript symbol column from ensembl id
                        for human and mouse data
fill_missing_abundance
                        Fill transcript abundance if missing from
                        sample-transcript pairs
filter                  Subset rows using column values
flybaseIDs              flybaseIDs
get_bibliography        Produces the bibliography list of your workflow
group_by                Group by one or more variables
identify_abundant       Identify abundant transcripts/genes
impute_missing_abundance
                        impute transcript abundance if missing from
                        sample-transcript pairs
inner_join              Inner join datasets
keep_abundant           Filter to keep only abundant transcripts/genes
keep_variable           Keep variable transcripts
log10_reverse_trans     log10_reverse_trans
logit_trans             logit scale
mutate                  Create, modify, and delete columns
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
rename                  Rename columns
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
rowwise                 Group input by rows
scale_abundance         Scale the counts of transcripts/genes
se                      SummarizedExperiment
se_mini                 SummarizedExperiment mini for vignette
summarise               Summarise each group to fewer rows
symbol_to_entrez        Get ENTREZ id from gene SYMBOL
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_cellularity
                        Add differential tissue composition information
                        to a tbl
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
                        Test of stratification of biological replicates
                        based on tissue composition, one cell-type at
                        the time, using Kaplan-meier curves.
tidybulk                Creates an annotated 'tidybulk' tibble from a
                        'tbl' or 'SummarizedExperiment' object
tidybulk_SAM_BAM        Creates a 'tt' object from a list of file names
                        of BAM/SAM
tximeta_summarizeToGene_object
                        Needed for tests
                        tximeta_summarizeToGene_object, It is
                        SummarizedExperiment from tximeta
unnest                  unnest
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
