# Friendly tidy wrappers for streamlined bulk transcriptional analysis

## Documentation for package ‘tidybulk’ version 0.99.23

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G I K L M N P R S T U X

## -- A --

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-method | adjust_abundance
adjust_abundance-method | adjust_abundance
adjust_abundance-method | adjust_abundance
adjust_abundance-method | adjust_abundance
adjust_abundance-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-method | aggregate_duplicates
aggregate_duplicates-method | aggregate_duplicates
aggregate_duplicates-method | aggregate_duplicates
aggregate_duplicates-method | aggregate_duplicates
aggregate_duplicates-method | aggregate_duplicates
arrange | Arrange rows by column values
arrange.default | Arrange rows by column values
as_matrix | Get matrix from tibble

## -- B --

bind | Efficiently bind multiple data frames by row and column
bind_cols | Efficiently bind multiple data frames by row and column
bind_rows | Efficiently bind multiple data frames by row and column
breast_tcga_mini | Data set

## -- C --

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-method | cluster_elements
cluster_elements-method | cluster_elements
cluster_elements-method | cluster_elements
cluster_elements-method | cluster_elements
cluster_elements-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

## -- D --

deconvolve_cellularity | Get cell type proportions from samples
deconvolve_cellularity-method | deconvolve_cellularity
deconvolve_cellularity-method | deconvolve_cellularity
deconvolve_cellularity-method | deconvolve_cellularity
deconvolve_cellularity-method | deconvolve_cellularity
deconvolve_cellularity-method | deconvolve_cellularity
distinct | distinct
drop_attr | Drop attribute to abject
drop_class | Remove class to abject

## -- E --

ensembl_symbol_mapping | Data set
ensembl_to_symbol | Add transcript symbol column from ensembl id for human and mouse data
ensembl_to_symbol-method | ensembl_to_symbol
ensembl_to_symbol-method | ensembl_to_symbol
ensembl_to_symbol-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

## -- F --

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

## -- G --

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_kmeans_bulk | Get K-mean clusters to a tibble
get_clusters_SNN_bulk | Get SNN shared nearest neighbour 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

## -- I --

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-method | impute_abundance
impute_abundance-method | impute_abundance
impute_abundance-method | impute_abundance
impute_abundance-method | impute_abundance
impute_abundance-method | impute_abundance
inner_join | Inner join datasets

## -- K --

keep_abundant | Filter abundant transcripts
keep_abundant-method | keep_abundant
keep_abundant-method | keep_abundant
keep_abundant-method | keep_abundant
keep_abundant-method | keep_abundant
keep_abundant-method | keep_abundant
keep_variable | Filter variable transcripts
keep_variable-method | keep_variable
keep_variable-method | keep_variable
keep_variable-method | keep_variable
keep_variable-method | keep_variable
keep_variable-method | keep_variable
keep_variable_transcripts | Identify variable genes for dimensionality reduction

## -- L --

left_join | Left join datasets

## -- M --

mutate | Create, modify, and delete columns

## -- N --

nest | nest

## -- P --

parse_formula | .formula parser
pivot_sample | Extract sampe-wise information
pivot_sample-method | pivot_sample
pivot_sample-method | pivot_sample
pivot_sample-method | pivot_sample
pivot_transcript | Extract transcript-wise information
pivot_transcript-method | pivot_transcript
pivot_transcript-method | pivot_transcript
pivot_transcript-method | pivot_transcript
prepend | From rlang deprecated

## -- R --

reduce_dimensions | Dimension reduction of the transcript abundance data
reduce_dimensions-method | reduce_dimensions
reduce_dimensions-method | reduce_dimensions
reduce_dimensions-method | reduce_dimensions
reduce_dimensions-method | reduce_dimensions
reduce_dimensions-method | reduce_dimensions
remove_redundancy | Drop redundant elements (e.g., samples) for which feature (e.g., transcript/gene) aboundances are correlated
remove_redundancy-method | remove_redundancy
remove_redundancy-method | remove_redundancy
remove_redundancy-method | remove_redundancy
remove_redundancy-method | remove_redundancy
remove_redundancy-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-method | rotate_dimensions
rotate_dimensions-method | rotate_dimensions
rotate_dimensions-method | rotate_dimensions
rotate_dimensions-method | rotate_dimensions
rotate_dimensions-method | rotate_dimensions
rowwise | Group input by rows
run_llsr | Perform linear equation system analysis through llsr

## -- S --

scale_abundance | Scale the counts of transcripts/genes
scale_abundance-method | scale_abundance
scale_abundance-method | scale_abundance
scale_abundance-method | scale_abundance
scale_abundance-method | scale_abundance
scale_abundance-method | scale_abundance
scale_design | Scale design matrix
se | SummarizedExperiment
select_closest_pairs | Sub function of remove_redundancy_elements_though_reduced_dimensions
se_mini | SummarizedExperiment mini for vignette
summarise | Summarise each group to fewer rows
symbol_to_entrez | Get ENTREZ id from gene SYMBOL

## -- T --

test_differential_abundance | Add differential transcription information to a tbl using edgeR.
test_differential_abundance-method | test_differential_abundance
test_differential_abundance-method | test_differential_abundance
test_differential_abundance-method | test_differential_abundance
test_differential_abundance-method | test_differential_abundance
test_differential_abundance-method | test_differential_abundance
test_gene_enrichment | analyse gene enrichment with EGSEA
test_gene_enrichment-method | test_gene_enrichment
test_gene_enrichment-method | test_gene_enrichment
test_gene_enrichment-method | test_gene_enrichment
test_gene_enrichment_bulk_EGSEA | Get gene enrichment analyses using EGSEA
tidybulk | Creates a 'tt' object from a 'tbl"
tidybulk-method | tidybulk
tidybulk-method | tidybulk
tidybulk-method | tidybulk
tidybulk-method | tidybulk
tidybulk_SAM_BAM | Creates a 'tt' object from a list of file names of BAM/SAM
tidybulk_SAM_BAM-method | tidybulk_SAM_BAM
tidybulk_to_SummarizedExperiment | tidybulk_to_SummarizedExperiment

## -- U --

ungroup | Group by one or more variables

## -- X --

X_cibersort | Cibersort reference