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Ramos, M, et al. (2017) Software for the Integration of Multiomics Experiments in Bioconductor Cancer Research 77:e39-e42. doi:10.1158/0008-5472.CAN-17-0344
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 2018-05-20T05:40:06-04:00.

Cao X, George EO, Wang M, Armstrong DB, Cheng C, Raimondi S, Rubnitz JE, Downing JR, Kundu M, Pounds SB. POST: a framework for set-based association analysis in high-dimensional data. Methods. doi:10.1016/j.ymeth.2018.05.011 (16 May 2018)
Bunnik EM, Cook KB, Varoquaux N, Batugedara G, Prudhomme J, Cort A, Shi L, Andolina C, Ross LS, Brady D, Fidock DA, Nosten F, Tewari R, Sinnis P, Ay F, Vert JP, Noble WS, Le Roch KG. Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages Nat Commun, 9, pp. 1910. doi:10.1038/s41467-018-04295-5 (15 May 2018)
Mackay A, Burford A, Molinari V, Jones DT, Izquierdo E, Brouwer-Visser J, Giangaspero F, Haberler C, Pietsch T, Jacques TS, Figarella-Branger D, Rodriguez D, Morgan PS, Raman P, Waanders AJ, Resnick AC, Massimino M, Garrè ML, Smith H, Capper D, Pfister SM, Würdinger T, Tam R, Garcia J, Thakur MD, Vassal G, Grill J, Jaspan T, Varlet P, Jones C. Molecular, Pathological, Radiological, and Immune Profiling of Non-brainstem Pediatric High-Grade Glioma from the HERBY Phase II Randomized Trial Cancer Cell, 33(5), pp. 829-842.e5. doi:10.1016/j.ccell.2018.04.004 (14 May 2018)
Pan Y, Lu L, Chen J, Zhong Y, Dai Z. Identification of potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma. Hereditas, 155, pp. 21. doi:10.1186/s41065-018-0061-9 (9 May 2018)
Zhang Y, Brady A, Jones C, Song Y, Darton TC, Jones C, Blohmke CJ, Pollard AJ, Magder LS, Fasano A, Sztein MB, Fraser CM. Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi mBio, 9(3), pp. e00686-18. doi:10.1128/mBio.00686-18 (8 May 2018)
Agrahari R, Foroushani A, Docking TR, Chang L, Duns G, Hudoba M, Karsan A, Zare H. Applications of Bayesian network models in predicting types of hematological malignancies. Sci Rep, 8(1), pp. 6951. doi:10.1038/s41598-018-24758-5 (3 May 2018)
Lun ATL, Pagès H, Smith ML. beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types. PLoS Comput Biol, 14(5), pp. e1006135. doi:10.1371/journal.pcbi.1006135 (3 May 2018)
Neller KC, Klenov A, Guzman JC, Hudak KA. Integration of the Pokeweed miRNA and mRNA Transcriptomes Reveals Targeting of Jasmonic Acid-Responsive Genes Front Plant Sci, 9, pp. 589. doi:10.3389/fpls.2018.00589 (3 May 2018)
Genovese LM, Geraci F, Corrado L, Mangano E, D'Aurizio R, Bordoni R, Severgnini M, Manzini G, De Bellis G, D'Alfonso S, Pellegrini M. A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies Front Genet, 9, pp. 155. doi:10.3389/fgene.2018.00155 (2 May 2018)
Fan Q, Liu B. Comprehensive analysis of a long noncoding RNA-associated competing endogenous RNA network in colorectal cancer Onco Targets Ther, 11, pp. 2453-2466. doi:10.2147/OTT.S158309 (1 May 2018)
Puigdevall P, Castelo R. GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor. Bioinformatics. doi:10.1093/bioinformatics/bty311 (26 April 2018)
Blokzijl F, Janssen R, van Boxtel R, Cuppen E. MutationalPatterns: comprehensive genome-wide analysis of mutational processes. Genome Med, 10(1), pp. 33. doi:10.1186/s13073-018-0539-0 (25 April 2018)
Dai Z, Tang H, Pan Y, Chen J, Li Y, Zhu J. Gene expression profiles and pathway enrichment analysis of human osteosarcoma cells exposed to sorafenib. FEBS Open Bio, 8(5), pp. 860-867. doi:10.1002/2211-5463.12428 (24 April 2018)
Yan A, Ban Y, Gao Z, Chen X, Wang L. PathwaySplice: An R package for unbiased pathway analysis of alternative splicing in RNA-Seq data. Bioinformatics. doi:10.1093/bioinformatics/bty317 (24 April 2018)
Angeletti C. A Method for the Interpretation of Flow Cytometry Data Using Genetic Algorithms J Pathol Inform, 9, pp. 16. doi:10.4103/jpi.jpi_76_17 (20 April 2018)
Wu W, Huang B, Yan Y, Zhong ZQ. Exploration of gene functions for esophageal squamous cell carcinoma using network-based guilt by association principle Braz J Med Biol Res, 51(6), pp. e6801. doi:10.1590/1414-431X20186801 (19 April 2018)
Cedoz PL, Prunello M, Brennan K, Gevaert O. MethylMix 2.0: an R package for identifying DNA methylation genes. Bioinformatics. doi:10.1093/bioinformatics/bty156 (14 April 2018)
Bonora E, Bianco F, Stanzani A, Giancola F, Astolfi A, Indio V, Evangelisti C, Martelli AM, Boschetti E, Lugaresi M, Ioannou A, Torresan F, Stanghellini V, Clavenzani P, Seri M, Moonen A, Van Beek K, Wouters M, Boeckxstaens GE, Zaninotto G, Mattioli S, De Giorgio R. INPP4B overexpression and c-KIT downregulation in human achalasia. Neurogastroenterol Motil, pp. e13346. doi:10.1111/nmo.13346 (11 April 2018)
Oghabian A, Greco D, Frilander MJ. IntEREst: intron-exon retention estimator. BMC Bioinformatics, 19(1), pp. 130. doi:10.1186/s12859-018-2122-5 (11 April 2018)

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