Publications

Featured

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).
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
Tippmann, S. (2015) Programming tools: Adventures with R. Nature 517: 109–110.
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

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2015-03-03T06:30:09-08:00.

Pelle KG, Oh K, Buchholz K, Narasimhan V, Joice R, Milner DA, Brancucci NM, Ma S, Voss TS, Ketman K, Seydel KB, Taylor TE, Barteneva NS, Huttenhower C, Marti M. Transcriptional profiling defines dynamics of parasite tissue sequestration during malaria infection Genome Med, 7(1), pp. 19. doi:10.1186/s13073-015-0133-7 (27 February 2015)
Hubbard A, Lewis CM, Yoshida K, Ramirez-Gonzalez RH, de Vallavieille-Pope C, Thomas J, Kamoun S, Bayles R, Uauy C, Saunders DG. Field pathogenomics reveals the emergence of a diverse wheat yellow rust population Genome Biol, 16(1), pp. 23. doi:10.1186/s13059-015-0590-8 (25 February 2015)
Panse C, Trachsel C, Grossmann J, Schlapbach R. specL - An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. Bioinformatics. doi:10.1093/bioinformatics/btv105 (23 February 2015)
Nakayama J, Watanabe K, Jiang J, Matsuda K, Chao SH, Haryono P, La-ongkham O, Sarwoko MA, Sujaya IN, Zhao L, Chen KT, Chen YP, Chiu HH, Hidaka T, Huang NX, Kiyohara C, Kurakawa T, Sakamoto N, Sonomoto K, Tashiro K, Tsuji H, Chen MJ, Leelavatcharamas V, Liao CC, Nitisinprasert S, Rahayu ES, Ren FZ, Tsai YC, Lee YK. Diversity in gut bacterial community of school-age children in Asia Sci Rep, 5, pp. 8397. doi:10.1038/srep08397 (23 February 2015)
Simões JM, Barata EN, Harris RM, O’Connell LA, Hofmann HA, Oliveira RF. Social odors conveying dominance and reproductive information induce rapid physiological and neuromolecular changes in a cichlid fish BMC Genomics, 16(1), pp. 114. doi:10.1186/s12864-015-1255-4 (22 February 2015)
Calusinska M, Hamilton C, Monsieurs P, Mathy G, Leys N, Franck F, Joris B, Thonart P, Hiligsmann S, Wilmotte A. Genome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009 Biotechnol Biofuels, 8, pp. 27. doi:10.1186/s13068-015-0203-5 (22 February 2015)
Narum SR, Campbell NR. Transcriptomic response to heat stress among ecologically divergent populations of redband trout BMC Genomics, 16(1), pp. 103. doi:10.1186/s12864-015-1246-5 (21 February 2015)
Han X, Yang Y, Yan H, Wang X, Qu L, Chen Y. Rumen Bacterial Diversity of 80 to 110-Day-Old Goats Using 16S rRNA Sequencing PLoS One, 10(2), pp. e0117811. doi:10.1371/journal.pone.0117811 (20 February 2015)
Castellano L, Rizzi E, Krell J, Di Cristina M, Galizi R, Mori A, Tam J, De Bellis G, Stebbing J, Crisanti A, Nolan T. The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNAs BMC Genomics, 16(1), pp. 100. doi:10.1186/s12864-015-1257-2 (19 February 2015)
Hendrickx DM, Jennen DG, Briedé JJ, Cavill R, de Kok TM, Kleinjans JC. Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study. Bioinformatics. doi:10.1093/bioinformatics/btv108 (19 February 2015)
Yang X, Koltes JE, Park CA, Chen D, Reecy JM. Gene Co-Expression Network Analysis Provides Novel Insights into Myostatin Regulation at Three Different Mouse Developmental Timepoints PLoS One, 10(2), pp. e0117607. doi:10.1371/journal.pone.0117607 (19 February 2015)
Zhao S, Zhang B. A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification BMC Genomics, 16(1), pp. 97. doi:10.1186/s12864-015-1308-8 (18 February 2015)
Yuan T, Jiao Y, de Jong S, Ophoff RA, Beck S, Teschendorff AE. An Integrative Multi-scale Analysis of the Dynamic DNA Methylation Landscape in Aging PLoS Genet, 11(2), pp. e1004996. doi:10.1371/journal.pgen.1004996 (18 February 2015)
Walker RA, Sharman PA, Miller CM, Lippuner C, Okoniewski M, Eichenberger RM, Ramakrishnan C, Brossier F, Deplazes P, Hehl AB, Smith NC. RNA Seq analysis of the Eimeria tenella gametocyte transcriptome reveals clues about the molecular basis for sexual reproduction and oocyst biogenesis BMC Genomics, 16(1), pp. 94. doi:10.1186/s12864-015-1298-6 (18 February 2015)
Griese M, Kirmeier HG, Liebisch G, Rauch D, Stückler F, Schmitz G, Zarbock R. Surfactant Lipidomics in Healthy Children and Childhood Interstitial Lung Disease PLoS One, 10(2), pp. e0117985. doi:10.1371/journal.pone.0117985 (18 February 2015)
Gatto L, Breckels LM, Naake T, Gibb S. Visualisation of proteomics data using R and Bioconductor. Proteomics. doi:10.1002/pmic.201400392 (18 February 2015)
Rodilla V, Dasti A, Huyghe M, Lafkas D, Laurent C, Reyal F, Fre S. Luminal Progenitors Restrict Their Lineage Potential during Mammary Gland Development PLoS Biol, 13(2), pp. e1002069. doi:10.1371/journal.pbio.1002069 (17 February 2015)
Dressaire C, Moreira RN, Barahona S, Alves de Matos AP, Arraiano CM. BolA Is a Transcriptional Switch That Turns Off Motility and Turns On Biofilm Development mBio, 6(1), pp. e02352-14. doi:10.1128/mBio.02352-14 (17 February 2015)
Steinhilber J, Bonin M, Walter M, Fend F, Bonzheim I, Quintanilla-Martinez L. Next-Generation Sequencing Identifies Deregulation of MicroRNAs Involved in Both Innate and Adaptive Immune Response in ALK+ ALCL PLoS One, 10(2), pp. e0117780. doi:10.1371/journal.pone.0117780 (17 February 2015)
Oshida K, Vasani N, Thomas RS, Applegate D, Rosen M, Abbott B, Lau C, Guo G, Aleksunes LM, Klaassen C, Corton JC. Identification of Modulators of the Nuclear Receptor Peroxisome Proliferator-Activated Receptor α (PPARα) in a Mouse Liver Gene Expression Compendium PLoS One, 10(2), pp. e0112655. doi:10.1371/journal.pone.0112655 (17 February 2015)

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