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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 2015-10-09T04:20:07-04:00.

Schmich F, Szczurek E, Kreibich S, Dilling S, Andritschke D, Casanova A, Low SH, Eicher S, Muntwiler S, Emmenlauer M, Rämö P, Conde-Alvarez R, von Mering C, Hardt WD, Dehio C, Beerenwinkel N. gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens. Genome Biol, 16(1), pp. 220. doi:10.1186/s13059-015-0783-1 (7 October 2015)
Wright ES. DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics, 16(1), pp. 322. doi:10.1186/s12859-015-0749-z (6 October 2015)
Blaha M, Nemcova L, Kepkova KV, Vodicka P, Prochazka R. Gene expression analysis of pig cumulus-oocyte complexes stimulated in vitro with follicle stimulating hormone or epidermal growth factor-like peptides Reprod Biol Endocrinol, 13, pp. 113. doi:10.1186/s12958-015-0112-2 (6 October 2015)
Larney C, Bailey TL, Koopman P. Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species BMC Dev Biol, 15, pp. 34. doi:10.1186/s12861-015-0085-6 (6 October 2015)
Wong EM, Joo JE, McLean CA, Baglietto L, English DR, Severi G, Hopper JL, Milne RL, FitzGerald LM, Giles GG, Southey MC. Tools for translational epigenetic studies involving formalin-fixed paraffin-embedded human tissue: applying the Infinium HumanMethyation450 Beadchip assay to large population-based studies BMC Res Notes, 8, pp. 543. doi:10.1186/s13104-015-1487-z (6 October 2015)
Noll JE, Vandyke K, Hewett DR, Mrozik KM, Bala RJ, Williams SA, Kok CH, Zannettino AC. PTTG1 expression is associated with hyperproliferative disease and poor prognosis in multiple myeloma J Hematol Oncol, 8, pp. 106. doi:10.1186/s13045-015-0209-2 (6 October 2015)
Lang S, Ugale A, Erlandsson E, Karlsson G, Bryder D, Soneji S. SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data BMC Bioinformatics, 16, pp. 320. doi:10.1186/s12859-015-0757-z (5 October 2015)
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)
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)
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)
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)
Johannessen B, Sveen A, Skotheim RI. TIN: An R Package for Transcriptome Instability Analysis. Cancer Inform, 14, pp. 109-112. doi:10.4137/CIN.S31363 (20 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)


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