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Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.
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). PMC4509590
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, and Smyth, GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucl. Acids Res; doi:10.1093/nar/gkv007
Love M, Huber W, and Anders S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550; doi:10.1186/s13059-014-0550-8
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


20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2015-10-07T03:40:07-04:00.

Calla B, Geib SM. MicroRNAs in the oriental fruit fly, Bactrocera dorsalis: extending Drosophilid miRNA conservation to the Tephritidae BMC Genomics, 16, pp. 740. doi:10.1186/s12864-015-1835-3 (5 October 2015)
Lips EH, Michaut M, Hoogstraat M, Mulder L, Besselink NJ, Koudijs MJ, Cuppen E, Voest EE, Bernards R, Nederlof PM, Wesseling J, Rodenhuis S, Wessels LF. Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response Breast Cancer Res, 17, pp. 134. doi:10.1186/s13058-015-0642-8 (3 October 2015)
Holl HM, Gao S, Fei Z, Andrews C, Brooks SA. Generation of a de novo transcriptome from equine lamellar tissue BMC Genomics, 16, pp. 739. doi:10.1186/s12864-015-1948-8 (3 October 2015)
Suomi T, Corthals GL, Nevalainen OS, Elo LL. Using peptide-level proteomics data for detecting differentially expressed proteins. J Proteome Res. doi:10.1021/acs.jproteome.5b00363 (2 October 2015)
Hardcastle TJ. Generalised empirical Bayesian methods for discovery of differential data in high-throughput biology. Bioinformatics. doi:10.1093/bioinformatics/btv569 (1 October 2015)
Lambirth KC, Whaley AM, Blakley IC, Schlueter JA, Bost KL, Loraine AE, Piller KJ. A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq BMC Biotechnol, 15, pp. 89. doi:10.1186/s12896-015-0207-z (1 October 2015)
Gel B, Díez-Villanueva A, Serra E, Buschbeck M, Peinado MA, Malinverni R. regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests. Bioinformatics. doi:10.1093/bioinformatics/btv562 (30 September 2015)
Phipson B, Maksimovic J, Oshlack A. missMethyl: an R package for analysing methylation data from Illumina's HumanMethylation450 platform. Bioinformatics. doi:10.1093/bioinformatics/btv560 (30 September 2015)
Sfakianaki P, Koumakis L, Sfakianakis S, Iatraki G, Zacharioudakis G, Graf N, Marias K, Tsiknakis M. Semantic biomedical resource discovery: a Natural Language Processing framework BMC Med Inform Decis Mak, 15, pp. 77. doi:10.1186/s12911-015-0200-4 (30 September 2015)
Freel KC, Krueger MC, Farasin J, Brochier-Armanet C, Barbe V, Andrès J, Cholley PE, Dillies MA, Jagla B, Koechler S, Leva Y, Magdelenat G, Plewniak F, Proux C, Coppée JY, Bertin PN, Heipieper HJ, Arsène-Ploetze F. Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas PLoS One, 10(9), pp. e0139011. doi:10.1371/journal.pone.0139011 (30 September 2015)
Hayes JE, Trynka G, Vijai J, Offit K, Raychaudhuri S, Klein RJ. Tissue-Specific Enrichment of Lymphoma Risk Loci in Regulatory Elements PLoS One, 10(9), pp. e0139360. doi:10.1371/journal.pone.0139360 (30 September 2015)
Wang Y, Huang L, Wu S, Jia Y, Yang Y, Luo L, Bi A, Fang M. Bioinformatics Analyses of the Role of Vascular Endothelial Growth Factor in Patients with Non-Small Cell Lung Cancer PLoS One, 10(9), pp. e0139285. doi:10.1371/journal.pone.0139285 (30 September 2015)
Kishore K, de Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, Ecker JR, Pelizzola M. methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. BMC Bioinformatics, 16(1), pp. 313. doi:10.1186/s12859-015-0742-6 (29 September 2015)
Bellot P, Olsen C, Salembier P, Oliveras-Vergés A, Meyer PE. NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference. BMC Bioinformatics, 16(1), pp. 312. doi:10.1186/s12859-015-0728-4 (29 September 2015)
Freytag S, Gagnon-Bartsch J, Speed TP, Bahlo M. Systematic noise degrades gene co-expression signals but can be corrected. BMC Bioinformatics, 16(1), pp. 309. doi:10.1186/s12859-015-0745-3 (24 September 2015)
Trutschel D, Schmidt S, Grosse I, Neumann S. Joint Analysis of Dependent Features within Compound Spectra Can Improve Detection of Differential Features Front Bioeng Biotechnol, 3, pp. 129. doi:10.3389/fbioe.2015.00129 (24 September 2015)
Tabanelli G, Vernocchi P, Patrignani F, Del Chierico F, Putignani L, Vinderola G, Reinheimer JA, Gardini F, Lanciotti R. Effects of sub-lethal high-pressure homogenization treatment on the outermost cellular structures and the volatile-molecule profiles of two strains of probiotic lactobacilli Front Microbiol, 6, pp. 1006. doi:10.3389/fmicb.2015.01006 (23 September 2015)
Zhang CH, Ma T, Luo WC, Xu JM, Liu JQ, Wan DS. Identification of 4CL Genes in Desert Poplars and Their Changes in Expression in Response to Salt Stress Genes (Basel), 6(3), pp. 901-917. doi:10.3390/genes6030901 (18 September 2015)
Xu Z, Niu L, Li L, Taylor JA. ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic Acids Res. doi:10.1093/nar/gkv907 (17 September 2015)
Suchiman HE, Slieker RC, Kremer D, Slagboom PE, Heijmans BT, Tobi EW. Design, measurement and processing of region-specific DNA methylation assays: the mass spectrometry-based method EpiTYPER Front Genet, 6, pp. 287. doi:10.3389/fgene.2015.00287 (17 September 2015)


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