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Amezquita, R.A., Lun, A.T.L., Becht, E. et al. Orchestrating single-cell analysis with Bioconductor. Nature Methods (2019) doi:10.1038/s41592-019-0654-x
Pasolli, E, et al. (2017) Accessible, curated metagenomic data through ExperimentHub Nature Methods 14, 1023–1024. doi:10.1038/nmeth.4468
Huber W, et al. (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods 12:115-121; doi:10.1038/nmeth.3252 (full-text free with registration).
Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi: 10.1371/journal.pcbi.1003118
Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2021-10-26T21:30:08-04:00.

Su S, Gouil Q, Blewitt ME, Cook D, Hickey PF, Ritchie ME. NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data. PLoS Comput Biol, 17(10), pp. e1009524. doi:10.1371/journal.pcbi.1009524 (25 October 2021)
Vanderaa C, Gatto L. Replication of single-cell proteomics data reveals important computational challenges. Expert Rev Proteomics, pp. 1-9. doi:10.1080/14789450.2021.1988571 (25 October 2021)
Wright ES. FindNonCoding: rapid and simple detection of non-coding RNAs in genomes. Bioinformatics. doi:10.1093/bioinformatics/btab708 (12 October 2021)
Castellano-Escuder P, Andrés-Lacueva C, Sánchez-Pla A. The fobitools framework: the first steps towards food enrichment analysis. Bioinformatics. doi:10.1093/bioinformatics/btab626 (2 October 2021)
Murphy AE, Schilder BM, Skene NG. MungeSumstats: A Bioconductor package for the standardisation and quality control of many GWAS summary statistics. Bioinformatics. doi:10.1093/bioinformatics/btab665 (2 October 2021)
Nystrom SL, McKay DJ. Memes: A motif analysis environment in R using tools from the MEME Suite. PLoS Comput Biol, 17(9), pp. e1008991. doi:10.1371/journal.pcbi.1008991 (27 September 2021)
Yue A, Chauve C, Libbrecht MW, Brinkman RR. Automated identification of maximal differential cell populations in flow cytometry data. Cytometry A. doi:10.1002/cyto.a.24503 (24 September 2021)
Bodein A, Scott-Boyer MP, Perin O, Lê Cao KA, Droit A. timeOmics: an R package for longitudinal multi-omics data integration. Bioinformatics. doi:10.1093/bioinformatics/btab664 (23 September 2021)
Huang S, Pang L, Wei C. Identification of a Four-Gene Signature With Prognostic Significance in Endometrial Cancer Using Weighted-Gene Correlation Network Analysis. Front Genet, 12, pp. 678780. doi:10.3389/fgene.2021.678780 (20 September 2021)
Cooley NP, Wright ES. Accurate annotation of protein coding sequences with IDTAXA. NAR Genom Bioinform, 3(3), pp. lqab080. doi:10.1093/nargab/lqab080 (16 September 2021)
Scherer M, Gasparoni G, Rahmouni S, Shashkova T, Arnoux M, Louis E, Nostaeva A, Avalos D, Dermitzakis ET, Aulchenko YS, Lengauer T, Lyons PA, Georges M, Walter J. Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR. Epigenetics Chromatin, 14(1), pp. 44. doi:10.1186/s13072-021-00415-6 (16 September 2021)
Skidmore ZL, Campbell KM, Cotto KC, Griffith M, Griffith OL. Exploring the Genomic Landscape of Cancer Patient Cohorts with GenVisR. Curr Protoc, 1(9), pp. e252. doi:10.1002/cpz1.252 (11 September 2021)
Liu F, Liu Y, Du Y, Li Y. MiRNA-130a promotes inflammation to accelerate atherosclerosis via the regulation of proliferator-activated receptor γ (PPARγ) expression. Anatol J Cardiol, 25(9), pp. 630-637. doi:10.5152/AnatolJCardiol.2021.56721 (10 September 2021)
Atta L, Sahoo A, Fan J. VeloViz: RNA velocity informed embeddings for visualizing cellular trajectories. Bioinformatics. doi:10.1093/bioinformatics/btab653 (9 September 2021)
Dankó B, Szikora P, Pór T, Szeifert A, Sebestyén E. SplicingFactory-splicing diversity analysis for transcriptome data. Bioinformatics. doi:10.1093/bioinformatics/btab648 (9 September 2021)
Borella M, Martello G, Risso D, Romualdi C. PsiNorm: a scalable normalization for single-cell RNA-seq data. Bioinformatics. doi:10.1093/bioinformatics/btab641 (9 September 2021)
Zheng Y, Cai B, Ren C, Xu H, Du W, Wu Y, Lin F, Zhang H, Quan R. Identification of immune related cells and crucial genes in the peripheral blood of ankylosing spondylitis by integrated bioinformatics analysis. PeerJ, 9, pp. e12125. doi:10.7717/peerj.12125 (7 September 2021)
Ghosh T, Philtron D, Zhang W, Kechris K, Ghosh D. Reproducibility of mass spectrometry based metabolomics data. BMC Bioinformatics, 22(1), pp. 423. doi:10.1186/s12859-021-04336-9 (7 September 2021)
Li Y, Qin J. A Two-Gene-Based Diagnostic Signature for Ruptured Intracranial Aneurysms. Front Cardiovasc Med, 8, pp. 671655. doi:10.3389/fcvm.2021.671655 (13 August 2021)
Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L, Fu X, Liu S, Bo X, Yu G. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (N Y), 2(3), pp. 100141. doi:10.1016/j.xinn.2021.100141 (1 July 2021)

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