X_cibersort             Cibersort reference
add_attr                Add attribute to abject
add_class               Add class to abject
add_scaled_counts_bulk.calcNormFactor
                        Calculate the norm factor with calcNormFactor
                        from limma
add_scaled_counts_bulk.get_low_expressed
                        Drop lowly tanscribed genes for TMM
                        normalization
adjust_abundance        Adjust transcript abundance for unwanted
                        variation
adjust_abundance,RangedSummarizedExperiment-method
                        adjust_abundance
adjust_abundance,SummarizedExperiment-method
                        adjust_abundance
adjust_abundance,spec_tbl_df-method
                        adjust_abundance
adjust_abundance,tbl_df-method
                        adjust_abundance
adjust_abundance,tidybulk-method
                        adjust_abundance
aggregate_duplicated_transcripts_bulk
                        Aggregates multiple counts from the same
                        samples (e.g., from isoforms) This function
                        aggregates counts over samples, concatenates
                        other character columns, and averages other
                        numeric columns
aggregate_duplicates    Aggregates multiple counts from the same
                        samples (e.g., from isoforms), concatenates
                        other character columns, and averages other
                        numeric columns
aggregate_duplicates,RangedSummarizedExperiment-method
                        aggregate_duplicates
aggregate_duplicates,SummarizedExperiment-method
                        aggregate_duplicates
aggregate_duplicates,spec_tbl_df-method
                        aggregate_duplicates
aggregate_duplicates,tbl_df-method
                        aggregate_duplicates
aggregate_duplicates,tidybulk-method
                        aggregate_duplicates
arrange                 Arrange rows by column values
as_matrix               Get matrix from tibble
bind                    Efficiently bind multiple data frames by row
                        and column
breast_tcga_mini        Data set
check_if_counts_is_na   Check whether there are NA counts
check_if_duplicated_genes
                        Check whether there are duplicated
                        genes/transcripts
check_if_wrong_input    Check whether there are NA counts
cluster_elements        Get clusters of elements (e.g., samples or
                        transcripts)
cluster_elements,RangedSummarizedExperiment-method
                        cluster_elements
cluster_elements,SummarizedExperiment-method
                        cluster_elements
cluster_elements,spec_tbl_df-method
                        cluster_elements
cluster_elements,tbl_df-method
                        cluster_elements
cluster_elements,tidybulk-method
                        cluster_elements
counts                  Example data set
counts_ensembl          Counts with ensembl annotation
counts_mini             Example data set reduced
create_tt_from_bam_sam_bulk
                        Convert bam/sam files to a tidy gene transcript
                        counts data frame
create_tt_from_tibble_bulk
                        Create tt object from tibble
deconvolve_cellularity
                        Get cell type proportions from samples
deconvolve_cellularity,RangedSummarizedExperiment-method
                        deconvolve_cellularity
deconvolve_cellularity,SummarizedExperiment-method
                        deconvolve_cellularity
deconvolve_cellularity,spec_tbl_df-method
                        deconvolve_cellularity
deconvolve_cellularity,tbl_df-method
                        deconvolve_cellularity
deconvolve_cellularity,tidybulk-method
                        deconvolve_cellularity
distinct                distinct
drop_attr               Drop attribute to abject
drop_class              Remove class to abject
ensembl_symbol_mapping
                        Data set
ensembl_to_symbol       Add transcript symbol column from ensembl id
                        for human and mouse data
ensembl_to_symbol,spec_tbl_df-method
                        ensembl_to_symbol
ensembl_to_symbol,tbl_df-method
                        ensembl_to_symbol
ensembl_to_symbol,tidybulk-method
                        ensembl_to_symbol
error_if_counts_is_na   Check whether there are NA counts
error_if_duplicated_genes
                        Check whether there are duplicated
                        genes/transcripts
error_if_log_transformed
                        Check whether a numeric vector has been log
                        transformed
error_if_wrong_input    Check whether there are NA counts
fill_NA_using_formula   This function is needed for DE in case the
                        matrix is not rectangular, but includes NA
fill_NA_with_row_median
                        This function is needed for DE in case the
                        matrix is not rectangular, but includes NA
filter                  Subset rows using column values
flybaseIDs              flybaseIDs
full_join               Full join datasets
get_abundance_norm_if_exists
                        Get column names either from user or from
                        attributes
get_adjusted_counts_for_unwanted_variation_bulk
                        Get adjusted count for some batch effect
get_cell_type_proportions
                        Get cell type proportions from cibersort
get_clusters_SNN_bulk   Get SNN shared nearest neighbour clusters to a
                        tibble
get_clusters_kmeans_bulk
                        Get K-mean clusters to a tibble
get_differential_transcript_abundance_bulk
                        Get differential transcription information to a
                        tibble using edgeR.
get_elements            Get column names either from user or from
                        attributes
get_elements_features   Get column names either from user or from
                        attributes
get_elements_features_abundance
                        Get column names either from user or from
                        attributes
get_reduced_dimensions_MDS_bulk
                        Get dimensionality information to a tibble
                        using MDS
get_reduced_dimensions_PCA_bulk
                        Get principal component information to a tibble
                        using PCA
get_reduced_dimensions_TSNE_bulk
                        Get principal component information to a tibble
                        using tSNE
get_rotated_dimensions
                        Get rotated dimensions of two principal
                        components or MDS dimension of choice, of an
                        angle
get_sample              Get column names either from user or from
                        attributes
get_sample_counts       Get column names either from user or from
                        attributes
get_sample_transcript   Get column names either from user or from
                        attributes
get_sample_transcript_counts
                        Get column names either from user or from
                        attributes
get_scaled_counts_bulk
                        Get a tibble with scaled counts using TMM
get_symbol_from_ensembl
                        after wget, this function merges hg37 and hg38
                        mapping data bases - Do not execute!
get_transcript          Get column names either from user or from
                        attributes
get_x_y_annotation_columns
                        get_x_y_annotation_columns
group_by                Group by one or more variables
ifelse2_pipe            This is a generalisation of ifelse that acceots
                        an object and return an objects
ifelse_pipe             This is a generalisation of ifelse that acceots
                        an object and return an objects
impute_abundance        Impute transcript abundance if missing from
                        sample-transcript pairs
impute_abundance,RangedSummarizedExperiment-method
                        impute_abundance
impute_abundance,SummarizedExperiment-method
                        impute_abundance
impute_abundance,spec_tbl_df-method
                        impute_abundance
impute_abundance,tbl_df-method
                        impute_abundance
impute_abundance,tidybulk-method
                        impute_abundance
inner_join              Inner join datasets
keep_abundant           Filter abundant transcripts
keep_abundant,RangedSummarizedExperiment-method
                        keep_abundant
keep_abundant,SummarizedExperiment-method
                        keep_abundant
keep_abundant,spec_tbl_df-method
                        keep_abundant
keep_abundant,tbl_df-method
                        keep_abundant
keep_abundant,tidybulk-method
                        keep_abundant
keep_variable           Filter variable transcripts
keep_variable,RangedSummarizedExperiment-method
                        keep_variable
keep_variable,SummarizedExperiment-method
                        keep_variable
keep_variable,spec_tbl_df-method
                        keep_variable
keep_variable,tbl_df-method
                        keep_variable
keep_variable,tidybulk-method
                        keep_variable
keep_variable_transcripts
                        Identify variable genes for dimensionality
                        reduction
left_join               Left join datasets
mutate                  Create, modify, and delete columns
nest                    nest
parse_formula           .formula parser
pivot_sample            Extract sampe-wise information
pivot_sample,spec_tbl_df-method
                        pivot_sample
pivot_sample,tbl_df-method
                        pivot_sample
pivot_sample,tidybulk-method
                        pivot_sample
pivot_transcript        Extract transcript-wise information
pivot_transcript,spec_tbl_df-method
                        pivot_transcript
pivot_transcript,tbl_df-method
                        pivot_transcript
pivot_transcript,tidybulk-method
                        pivot_transcript
prepend                 From rlang deprecated
reduce_dimensions       Dimension reduction of the transcript abundance
                        data
reduce_dimensions,RangedSummarizedExperiment-method
                        reduce_dimensions
reduce_dimensions,SummarizedExperiment-method
                        reduce_dimensions
reduce_dimensions,spec_tbl_df-method
                        reduce_dimensions
reduce_dimensions,tbl_df-method
                        reduce_dimensions
reduce_dimensions,tidybulk-method
                        reduce_dimensions
remove_redundancy       Drop redundant elements (e.g., samples) for
                        which feature (e.g., transcript/gene)
                        aboundances are correlated
remove_redundancy,RangedSummarizedExperiment-method
                        remove_redundancy
remove_redundancy,SummarizedExperiment-method
                        remove_redundancy
remove_redundancy,spec_tbl_df-method
                        remove_redundancy
remove_redundancy,tbl_df-method
                        remove_redundancy
remove_redundancy,tidybulk-method
                        remove_redundancy
remove_redundancy_elements_though_reduced_dimensions
                        Identifies the closest pairs in a MDS contaxt
                        and return one of them
remove_redundancy_elements_through_correlation
                        Drop redundant elements (e.g., samples) for
                        which feature (e.g., genes) aboundances are
                        correlated
rename                  Rename columns
right_join              Right join datasets
rotate_dimensions       Rotate two dimensions (e.g., principal
                        components) of an arbitrary angle
rotate_dimensions,RangedSummarizedExperiment-method
                        rotate_dimensions
rotate_dimensions,SummarizedExperiment-method
                        rotate_dimensions
rotate_dimensions,spec_tbl_df-method
                        rotate_dimensions
rotate_dimensions,tbl_df-method
                        rotate_dimensions
rotate_dimensions,tidybulk-method
                        rotate_dimensions
rowwise                 Group input by rows
run_llsr                Perform linear equation system analysis through
                        llsr
scale_abundance         Scale the counts of transcripts/genes
scale_abundance,RangedSummarizedExperiment-method
                        scale_abundance
scale_abundance,SummarizedExperiment-method
                        scale_abundance
scale_abundance,spec_tbl_df-method
                        scale_abundance
scale_abundance,tbl_df-method
                        scale_abundance
scale_abundance,tidybulk-method
                        scale_abundance
scale_design            Scale design matrix
se                      SummarizedExperiment
se_mini                 SummarizedExperiment mini for vignette
select_closest_pairs    Sub function of
                        remove_redundancy_elements_though_reduced_dimensions
summarise               Summarise each group to fewer rows
symbol_to_entrez        Get ENTREZ id from gene SYMBOL
test_differential_abundance
                        Add differential transcription information to a
                        tbl using edgeR.
test_differential_abundance,RangedSummarizedExperiment-method
                        test_differential_abundance
test_differential_abundance,SummarizedExperiment-method
                        test_differential_abundance
test_differential_abundance,spec_tbl_df-method
                        test_differential_abundance
test_differential_abundance,tbl_df-method
                        test_differential_abundance
test_differential_abundance,tidybulk-method
                        test_differential_abundance
test_gene_enrichment    analyse gene enrichment with EGSEA
test_gene_enrichment,spec_tbl_df-method
                        test_gene_enrichment
test_gene_enrichment,tbl_df-method
                        test_gene_enrichment
test_gene_enrichment,tidybulk-method
                        test_gene_enrichment
test_gene_enrichment_bulk_EGSEA
                        Get gene enrichment analyses using EGSEA
tidybulk                Creates a 'tt' object from a 'tbl"
tidybulk,RangedSummarizedExperiment-method
                        tidybulk
tidybulk,SummarizedExperiment-method
                        tidybulk
tidybulk,spec_tbl_df-method
                        tidybulk
tidybulk,tbl_df-method
                        tidybulk
tidybulk_SAM_BAM        Creates a 'tt' object from a list of file names
                        of BAM/SAM
tidybulk_SAM_BAM,character,character-method
                        tidybulk_SAM_BAM
tidybulk_to_SummarizedExperiment
                        tidybulk_to_SummarizedExperiment
