# Brings transcriptomics to the tidyverse

## Documentation for package ‘tidybulk’ version 1.18.0

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

## Help Pages

.describe_transcript_SE | Get DESCRIPTION from gene SYMBOL for Human and Mouse
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 | Arrange rows by column values
as_matrix | Get matrix from tibble
as_SummarizedExperiment | as_SummarizedExperiment
as_SummarizedExperiment-method | as_SummarizedExperiment
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)
cluster_elements-method | Get clusters of elements (e.g., samples or transcripts)
counts_ensembl | Counts with ensembl annotation
deconvolve_cellularity | Get cell type proportions from samples
deconvolve_cellularity-method | Get cell type proportions from samples
describe_transcript | Get DESCRIPTION from gene SYMBOL for Human and Mouse
describe_transcript-method | 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
ensembl_to_symbol-method | Add transcript symbol column from ensembl id for human and mouse data
fill_missing_abundance | Fill transcript abundance if missing from sample-transcript pairs
fill_missing_abundance-method | Fill transcript abundance if missing from sample-transcript pairs
filter | Subset rows using column values
flybaseIDs | flybaseIDs
full_join | Inner join datasets
get_bibliography | Produces the bibliography list of your workflow
get_bibliography-method | Produces the bibliography list of your workflow
group_by | Group by one or more variables
identify_abundant | find abundant transcripts
identify_abundant-method | find abundant transcripts
impute_missing_abundance | impute transcript abundance if missing from sample-transcript pairs
impute_missing_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
log10_reverse_trans | log10_reverse_trans
logit_trans | logit scale
mutate | Create, modify, and delete columns
nest | unnest
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
quantile_normalise_abundance | Normalise by quantiles the counts of transcripts/genes
quantile_normalise_abundance-method | Normalise by quantiles the counts of transcripts/genes
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) abundances are correlated
remove_redundancy-method | 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-method | Resolve Complete Confounders of Non-Interest
right_join | Inner 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 | Perform differential transcription testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2
test_differential_abundance-method | 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_differential_cellularity-method | Add differential tissue composition information to a tbl
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
test_gene_rank | analyse gene rank with GSEA
test_gene_rank-method | 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.
test_stratification_cellularity-method | 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-method | 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
tidybulk_SAM_BAM-method | 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
X_cibersort | Cibersort reference