Package: tidybulk 2.3.0

Stefano Mangiola

tidybulk: Brings transcriptomics to the tidyverse

This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.

Authors:Stefano Mangiola [aut, cre], Maria Doyle [ctb]

tidybulk_2.3.0.tar.gz
tidybulk_2.3.0.zip(r-4.7)tidybulk_2.3.0.zip(r-4.6)tidybulk_2.3.0.zip(r-4.5)
tidybulk_2.3.0.tgz(r-4.6-any)tidybulk_2.3.0.tgz(r-4.5-any)
tidybulk_2.3.0.tar.gz(r-4.7-any)tidybulk_2.3.0.tar.gz(r-4.6-any)
tidybulk_2.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
tidybulk/json (API)

# Install 'tidybulk' in R:
install.packages('tidybulk', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stemangiola/tidybulk/issues

Datasets:

On BioConductor:tidybulk-2.3.0(bioc 3.24)tidybulk-2.2.0(bioc 3.23)

assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomicsbioconductorbulk-transcriptional-analysesdeseq2differential-expressionedgerensembl-idsentrezgene-symbolsgseamds-dimensionspcapiperedundancytibbletidytidy-datatidyversetranscriptstsne

10.31 score 180 stars 1 packages 208 scripts 621 downloads 2 mentions 31 exports 82 dependencies

Last updated from:a7e6f20fe6. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR422
linux-devel-x86_64NOTE1003
source / vignettesOK1345
linux-release-x86_64NOTE1083
macos-release-arm64NOTE504
macos-oldrel-arm64NOTE580
windows-develNOTE3471
windows-releaseNOTE3099
windows-oldrelNOTE3484
wasm-releaseOK409

Exports:adjust_abundanceaggregate_duplicatesas_matrixas_SummarizedExperimentcluster_elementsdeconvolve_cellularitydescribe_transcriptfill_missing_abundanceget_bibliographyget_X_cibersortidentify_abundantimpute_missing_abundancekeep_abundantkeep_variablelog10_reverse_translogit_transpivot_samplepivot_transcriptquantile_normalise_abundancereduce_dimensionsremove_redundancyresolve_complete_confounders_of_non_interestrotate_dimensionsscale_abundancescale_x_log10_reversescale_y_log10_reversetest_differential_abundancetest_differential_expressiontest_gene_enrichmenttest_gene_overrepresentationtest_gene_rank

Dependencies:abindaskpassbase64encBiobaseBiocGenericsbslibcachemclicpp11crayoncrosstalkcurldata.tableDelayedArraydigestdplyrevaluatefarverfastmapfontawesomefsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexttserviceutf8vctrsviridisLitewithrxfunXVectoryaml

tidybulk: An R tidy framework for modular transcriptomic data analysis

Stefano Mangiola

Rendered fromintroduction.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2025-09-15
Started: 2019-09-11

Side-by-side comparison with standard interfaces

Stefano Mangiola

Rendered fromcomparison_coding.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2025-09-13
Started: 2025-08-30

Readme and manuals

Help Manual

Help pageTopics
Adjust transcript abundance for unwanted variationadjust_abundance adjust_abundance,RangedSummarizedExperiment-method adjust_abundance,SummarizedExperiment-method
Aggregates multiple counts from the same samples (e.g., from isoforms), concatenates other character columns, and averages other numeric columnsaggregate_duplicates aggregate_duplicates,RangedSummarizedExperiment-method aggregate_duplicates,SummarizedExperiment-method
Get matrix from tibbleas_matrix
as_SummarizedExperimentas_SummarizedExperiment as_SummarizedExperiment,tbl_df-method
Get clusters of elements (e.g., samples or transcripts)cluster_elements cluster_elements,RangedSummarizedExperiment-method cluster_elements,SummarizedExperiment-method
Get cell type proportions from samplesdeconvolve_cellularity deconvolve_cellularity,RangedSummarizedExperiment-method deconvolve_cellularity,SummarizedExperiment-method
Get DESCRIPTION from gene SYMBOL for Human and Mouse.describe_transcript_SE describe_transcript describe_transcript,RangedSummarizedExperiment-method describe_transcript,SummarizedExperiment-method
Fill transcript abundance if missing from sample-transcript pairsfill_missing_abundance
Produces the bibliography list of your workflowget_bibliography get_bibliography,RangedSummarizedExperiment-method get_bibliography,SummarizedExperiment-method
Get Cibersort reference dataget_X_cibersort
Identify abundant transcripts/genesidentify_abundant identify_abundant,RangedSummarizedExperiment-method identify_abundant,SummarizedExperiment-method
impute transcript abundance if missing from sample-transcript pairsimpute_missing_abundance impute_missing_abundance,RangedSummarizedExperiment-method impute_missing_abundance,SummarizedExperiment-method
Filter to keep only abundant transcripts/geneskeep_abundant
keep_abundantkeep_abundant,RangedSummarizedExperiment-method
keep_abundantkeep_abundant,SummarizedExperiment-method
Keep variable transcriptskeep_variable keep_variable,RangedSummarizedExperiment-method keep_variable,SummarizedExperiment-method
Log10 reverse transformation for ggplot2log10_reverse_trans
logit scalelogit_trans
Extract sample-wise informationpivot_sample pivot_sample,RangedSummarizedExperiment-method pivot_sample,SummarizedExperiment-method
Extract transcript-wise informationpivot_transcript pivot_transcript,RangedSummarizedExperiment-method pivot_transcript,SummarizedExperiment-method
Normalise by quantiles the counts of transcripts/genesquantile_normalise_abundance quantile_normalise_abundance,RangedSummarizedExperiment-method quantile_normalise_abundance,SummarizedExperiment-method
Dimension reduction of the transcript abundance datareduce_dimensions reduce_dimensions,RangedSummarizedExperiment-method reduce_dimensions,SummarizedExperiment-method
Drop redundant elements (e.g., samples) for which feature (e.g., transcript/gene) abundances are correlatedremove_redundancy remove_redundancy,RangedSummarizedExperiment-method remove_redundancy,SummarizedExperiment-method
Resolve Complete Confounders of Non-Interestresolve_complete_confounders_of_non_interest
resolve_complete_confounders_of_non_interestresolve_complete_confounders_of_non_interest,RangedSummarizedExperiment-method resolve_complete_confounders_of_non_interest,SummarizedExperiment-method
Rotate two dimensions (e.g., principal components) of an arbitrary anglerotate_dimensions rotate_dimensions,RangedSummarizedExperiment-method rotate_dimensions,SummarizedExperiment-method
Scale the counts of transcripts/genesscale_abundance scale_abundance,RangedSummarizedExperiment-method scale_abundance,SummarizedExperiment-method
scale_x_log10_reversescale_x_log10_reverse
scale_y_log10_reversescale_y_log10_reverse
Perform differential transcription testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2test_differential_abundance test_differential_abundance,RangedSummarizedExperiment-method test_differential_abundance,SummarizedExperiment-method
Perform differential expression testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2test_differential_expression test_differential_expression,RangedSummarizedExperiment-method test_differential_expression,SummarizedExperiment-method
analyse gene enrichment with EGSEAtest_gene_enrichment test_gene_enrichment,RangedSummarizedExperiment-method test_gene_enrichment,SummarizedExperiment-method
analyse gene over-representation with GSEAtest_gene_overrepresentation test_gene_overrepresentation,RangedSummarizedExperiment-method test_gene_overrepresentation,SummarizedExperiment-method
analyse gene rank with GSEAtest_gene_rank test_gene_rank,RangedSummarizedExperiment-method test_gene_rank,SummarizedExperiment-method
test_stratification_cellularitytest_stratification_cellularity,RangedSummarizedExperiment-method test_stratification_cellularity,SummarizedExperiment-method
Needed for tests tximeta_summarizeToGene_object, It is SummarizedExperiment from tximetatximeta_summarizeToGene_object
Needed for vignette vignette_manuscript_signature_boxplotvignette_manuscript_signature_boxplot
Needed for vignette vignette_manuscript_signature_tsnevignette_manuscript_signature_tsne
Needed for vignette vignette_manuscript_signature_tsne2vignette_manuscript_signature_tsne2
Cibersort referenceX_cibersort