ArticleGenome biology2021
tidybulk: an R tidy framework for modular transcriptomic data analysis.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Efficient and Tidy Manipulation of Annotated Matrix Data with plyxp.bioRxiv : the preprint server for biology · 2026Article
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- tidyexposomics: integrated exposure-omics analysis powered by tidy principles.Bioinformatics advances · 2026Article
- Exploring transcriptomic and genomic differences between susceptible and resistant fetal pigs to maternal PRRSV infection at late gestation.Veterinary research · 2025Article
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- Human neural organoid microphysiological systems show the building blocks necessary for basic learning and memory.Communications biology · 2025Article
- SinoMedminer: an R package and shiny application for mining and visualizing traditional Chinese medicine herbal formulas.Chinese medicine · 2025Article
- Circulating immune cells exhibit distinct traits linked to metastatic burden in breast cancer.Breast cancer research : BCR · 2025Article
- Article
- Microglia-containing neural organoids as brain microphysiological systems for long-term culture.Frontiers in cellular neuroscience · 2025Article
- The tidyomics ecosystem: enhancing omic data analyses.Nature methods · 2024Article
- ThebioRxiv : the preprint server for biology · 2024Article
- A multi-organ map of the human immune system across age, sex and ethnicity.bioRxiv : the preprint server for biology · 2024Article
- Transcriptional signature of CD56Frontiers in immunology · 2024Article
- cellsig plug-in enhances CIBERSORTx signature selection for multidataset transcriptomes with sparse multilevel modelling.Bioinformatics (Oxford, England) · 2023Article
- PFKP is a prospective prognostic, diagnostic, immunological and drug sensitivity predictor across pan-cancer.Scientific reports · 2023Article
- sccomp: Robust differential composition and variability analysis for single-cell data.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Taurine deficiency as a driver of aging.Science (New York, N.Y.) · 2023Article
- bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing.Bioinformatics (Oxford, England) · 2023Article
- Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently, efforts have been made toward the harmonization of transcriptomic data structures and workflows using the concept of data tidiness, to facilitate modularisation. We present tidybulk, a modular framework for bulk transcriptional analyses that introduces a tidy transcriptomic data structure paradigm and analysis grammar. Tidybulk covers a wide variety of analysis procedures and integrates a large ecosystem of publicly available analysis algorithms under a common framework. Tidybulk decreases coding burden, facilitates reproducibility, increases efficiency for expert users, lowers the learning curve for inexperienced users, and bridges transcriptional data analysis with the tidyverse. Tidybulk is available at R/Bioconductor bioconductor.org/packages/tidybulk .
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