Brings transcriptomics to the tidyverse

Documentation for package ‘tidybulk’ version 1.0.2

Help Pages

adjust_abundance	Adjust transcript abundance for unwanted variation
adjust_abundance-method	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
aggregate_duplicates-method	Aggregates multiple counts from the same samples (e.g., from isoforms), concatenates other character columns, and averages other numeric columns
arrange	drplyr-methods
arrange.default	drplyr-methods
as_matrix	Get matrix from tibble
bind	Efficiently bind multiple data frames by row and column
bind_cols	drplyr-methods
bind_rows	drplyr-methods
breast_tcga_mini	Data set
cluster_elements	Get clusters of elements (e.g., samples or transcripts)
cluster_elements-method	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
deconvolve_cellularity-method	Get cell type proportions from samples
distinct	distinct
ensembl_symbol_mapping	Data set
ensembl_to_symbol	Add transcript symbol column from ensembl id for human and mouse data
ensembl_to_symbol-method	Add transcript symbol column from ensembl id for human and mouse data
filter	Subset rows using column values
flybaseIDs	flybaseIDs
full_join	Full join datasets
group_by	Group by one or more variables
impute_abundance	Impute transcript abundance if missing from sample-transcript pairs
impute_abundance-method	Impute transcript abundance if missing from sample-transcript pairs
inner_join	Inner join datasets
keep_abundant	Keep abundant transcripts
keep_abundant-method	Keep abundant transcripts
keep_variable	Keep variable transcripts
keep_variable-method	Keep variable transcripts
left_join	Left join datasets
mutate	Create, modify, and delete columns
nest	nest
nest.default	nest
nest.tidybulk	nest
pivot_sample	Extract sample-wise information
pivot_sample-method	Extract sample-wise information
pivot_transcript	Extract transcript-wise information
pivot_transcript-method	Extract transcript-wise information
reduce_dimensions	Dimension reduction of the transcript abundance data
reduce_dimensions-method	Dimension reduction of the transcript abundance data
remove_redundancy	Drop redundant elements (e.g., samples) for which feature (e.g., transcript/gene) aboundances are correlated
remove_redundancy-method	Drop redundant elements (e.g., samples) for which feature (e.g., transcript/gene) 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 two dimensions (e.g., principal components) of an arbitrary angle
rowwise	Group input by rows
scale_abundance	Scale the counts of transcripts/genes
scale_abundance-method	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	Add differential transcription information to a tbl using edgeR.
test_differential_abundance-method	Add differential transcription information to a tbl using edgeR.
test_gene_enrichment	analyse gene enrichment with EGSEA
test_gene_enrichment-method	analyse gene enrichment with EGSEA
test_gene_overrepresentation	analyse gene over-representation with GSEA
test_gene_overrepresentation-method	analyse gene over-representation with GSEA
tidybulk	Creates a 'tt' object from a 'tbl"
tidybulk-method	Creates a 'tt' object from a 'tbl"
tidybulk_SAM_BAM	Creates a 'tt' object from a list of file names of BAM/SAM
tidybulk_SAM_BAM-method	Creates a 'tt' object from a list of file names of BAM/SAM
ungroup	drplyr-methods
X_cibersort	Cibersort reference