tidybulk: an R tidy framework for modular transcriptomic data analysis

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...

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Bibliographic Details
Published inGenome Biology Vol. 22; no. 1; pp. 42 - 15
Main Authors Mangiola, Stefano, Molania, Ramyar, Dong, Ruining, Doyle, Maria A, Papenfuss, Anthony T
Format Journal Article
LanguageEnglish
Published England BioMed Central 22.01.2021
BMC
Subjects
Algorithms
Annotations
Computational Biology - methods
Data Analysis
Ecosystem
Ecosystems
Gene Expression Profiling - methods
Genes
Genetic engineering
Genomics
Genomics - methods
Grammar
Metadata
Packaging
Principal components analysis
Reproducibility of Results
Software
Transcription
Transcriptome
Visualization
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Summary: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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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-020-02233-7