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                 drplyr-methods
as_matrix               Get matrix from tibble
bind                    Efficiently bind multiple data frames by row
                        and column
breast_tcga_mini        Data set
cluster_elements        Get clusters of elements (e.g., samples or
                        transcripts)
counts                  Example data set
counts_ensembl          Counts with ensembl annotation
counts_mini             Example data set reduced
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
full_join               Full join datasets
get_bibliography        Produces the bibliography list of your workflow
group_by                Group by one or more variables
identify_abundant       find abundant transcripts
impute_missing_abundance
                        impute transcript abundance if missing from
                        sample-transcript pairs
inner_join              Inner join datasets
keep_abundant           Keep abundant transcripts
keep_variable           Keep variable transcripts
left_join               Left join datasets
log10_reverse_trans     log10_reverse_trans
logit_trans             logit scale
mutate                  Create, modify, and delete columns
parse_formula_survival
                        Formula parser with survival
pivot_sample            Extract sample-wise information
pivot_transcript        Extract transcript-wise information
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
right_join              Right join datasets
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_deseq2_df          SummarizedExperiment mini for vignette
test_differential_abundance
                        Perform differential transcription testing
                        using edgeR QLT, edgeR LR, limma-voom 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
tidybulk                Creates a 'tt' object from a 'tbl' or
                        'SummarizedExperiment' object
tidybulk_SAM_BAM        Creates a 'tt' object from a list of file names
                        of BAM/SAM
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
