Everything about Bioconductor

🧭 Start here: a 6-step reading path

1. Read the overview: BioconductorA 5-minute orientation
2. Skim a recent paper: microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualizationInfluential work since 2022
3. Pick up a classic book: Bioconductor case studiesThe most-reprinted book on the subject
4. Read the landmark paper: edgeR : a Bioconductor package for differential expression analysis of digital gene expression dataCited 41,310 times
5. Go sideways: List of RNA-Seq bioinformatics toolsA closely related topic
6. Go sideways: RNA-SeqA closely related topic

🏆 Landmark papers (most cited)

• edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

  Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth · 2009 · Bioinformatics · 41,310 citations

• Bioconductor: open software development for computational biology and bioinformatics

  Robert C Gentleman, Vincent J Carey, Douglas M Bates · 2004 · Genome Biology · 10,507 citations

• ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

  Guangchuang Yu, Li-Gen Wang, Qing-Yu He · 2015 · Bioinformatics · 4,610 citations

• Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

  Steffen Durinck, Paul T Spellman, Ewan Birney · 2009 · Nature Protocols · 4,404 citations

• Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

  Martin J. Aryee, Andrew E. Jaffe, Hector Corrada-Bravo · 2014 · Bioinformatics · 4,250 citations

• TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

  Antonio Colaprico, Tiago C. Silva, Catharina Olsen · 2015 · Nucleic Acids Research · 3,837 citations

• Orchestrating high-throughput genomic analysis with Bioconductor

  Wolfgang Huber, Vincent J Carey, Robert Gentleman · 2015 · Nature Methods · 3,722 citations

• GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor

  Sean Davis, Paul S. Meltzer · 2007 · Bioinformatics · 2,926 citations

🆕 Influential since 2022

• microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization

  Yang Cao, Qingyang Dong, Dan Wang · 2022 · Bioinformatics · 465 citations

• SimplifyEnrichment : A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results

  Zuguang Gu, Daniel Hübschmann · 2022 · Genomics, Proteomics & Bioinformatics · 297 citations

• rGREAT : an R/bioconductor package for functional enrichment on genomic regions

  Zuguang Gu, Daniel Hübschmann · 2022 · Bioinformatics · 198 citations

• spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

  Brenda Pardo, Abby Spangler, Lukas M. Weber · 2022 · BMC Genomics · 168 citations

• SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

  Dario Righelli, Lukas M Weber, Helena L Crowell · 2022 · Bioinformatics · 150 citations

📚 Books worth reading

• Bioconductor case studiesWolfgang Huber, Robert Gentleman · 2008
• Bioinformatics and computational biology solutions using R and BioconductorRobert Gentleman · 2005
• Statistics and data analysis for microarrays using R and BioconductorSorin Drăghici · 2012

Ranked by number of editions on Open Library, a rough measure of how lasting a book is.

🔗 Related topics

• List of RNA-Seq bioinformatics tools RNA-Seq is a technique that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. This…
• RNA-Seq RNA-Seq (short for RNA sequencing) is a next-generation sequencing (NGS) technique used to quantify and identify RNA molecules in a biological sample,…
• Transcriptomics technologies Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content…
• MA plot Within computational biology, an MA plot is an application of a Bland–Altman plot for visual representation of genomic data. The plot visualizes the differences…
• Metatranscriptomics Metatranscriptomics is the set of techniques used to study gene expression of microbes within natural environments, i.e., the metatranscriptome. While…
• Alicia Oshlack Alicia Yinema Kate Nungarai Oshlack is an Australian bioinformatician and is Co-Head of Computational Biology at the Peter MacCallum Cancer Centre in Melbourne…
• Sequence analysis In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand…
• DESeq2 DESeq2 is a software package in the field of bioinformatics and computational biology for the statistical programming language R. It is primarily employed…