Brings transcriptomics to the tidyverse

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Documentation for package ‘tidybulk’ version 1.10.1

• 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	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_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
counts_SE	Needed for vignette counts_SE
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
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
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_deseq2_df	SummarizedExperiment mini for vignette
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