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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
Kannan L, et al. (2015). Public data and open source tools for multi-assay genomic investigation of disease. Brief Bioinform. doi:10.1093/bib/bbv080
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

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2017-03-29T19:40:09-04:00.

Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M. SC3: consensus clustering of single-cell RNA-seq data. Nat Methods. doi:10.1038/nmeth.4236 (27 March 2017)
Noguera-Julian M, Guillén Y, Peterson J, Reznik D, Harris EV, Joseph SJ, Rivera J, Kannanganat S, Amara R, Nguyen ML, Mutembo S, Paredes R, Read TD, Marconi VC. Oral microbiome in HIV-associated periodontitis. Medicine (Baltimore), 96(12), pp. e5821. doi:10.1097/MD.0000000000005821 (23 March 2017)
Dey KK, Hsiao CJ, Stephens M. Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS Genet, 13(3), pp. e1006599. doi:10.1371/journal.pgen.1006599 (23 March 2017)
Yu D, Lim J, Wang X, Liang F, Xiao G. Enhanced construction of gene regulatory networks using hub gene information BMC Bioinformatics, 18, pp. 186. doi:10.1186/s12859-017-1576-1 (23 March 2017)
Skogholt AH, Ryeng E, Erlandsen SE, Skorpen F, Schønberg SA, Sætrom P. Gene expression differences between PAXgene and Tempus blood RNA tubes are highly reproducible between independent samples and biobanks BMC Res Notes, 10, pp. 136. doi:10.1186/s13104-017-2455-6 (23 March 2017)
Wu N, Zhu Q, Chen B, Gao J, Xu Z, Li D. High-throughput sequencing of pituitary and hypothalamic microRNA transcriptome associated with high rate of egg production BMC Genomics, 18, pp. 255. doi:10.1186/s12864-017-3644-3 (23 March 2017)
Kheirallah AK, de Moor CH, Faiz A, Sayers I, Hall IP. Lung function associated gene Integrator Complex subunit 12 regulates protein synthesis pathways BMC Genomics, 18, pp. 248. doi:10.1186/s12864-017-3628-3 (23 March 2017)
Taroni JN, Greene CS, Martyanov V, Wood TA, Christmann RB, Farber HW, Lafyatis RA, Denton CP, Hinchcliff ME, Pioli PA, Mahoney JM, Whitfield ML. A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis Genome Med, 9, pp. 27. doi:10.1186/s13073-017-0417-1 (23 March 2017)
Bradley PH, Pollard KS. Proteobacteria explain significant functional variability in the human gut microbiome Microbiome, 5, pp. 36. doi:10.1186/s40168-017-0244-z (23 March 2017)
Soto-Suárez M, Baldrich P, Weigel D, Rubio-Somoza I, San Segundo B. The Arabidopsis miR396 mediates pathogen-associated molecular pattern-triggered immune responses against fungal pathogens Sci Rep, 7, pp. 44898. doi:10.1038/srep44898 (23 March 2017)
Härtl K, Denton A, Franz-Oberdorf K, Hoffmann T, Spornraft M, Usadel B, Schwab W. Early metabolic and transcriptional variations in fruit of natural white-fruited Fragaria vesca genotypes Sci Rep, 7, pp. 45113. doi:10.1038/srep45113 (22 March 2017)
Solis NV, Swidergall M, Bruno VM, Gaffen SL, Filler SG. The Aryl Hydrocarbon Receptor Governs Epithelial Cell Invasion during Oropharyngeal Candidiasis mBio, 8(2), pp. e00025-17. doi:10.1128/mBio.00025-17 (21 March 2017)
Paquet ER, Lesurf R, Tofigh A, Dumeaux V, Hallett MT. Detecting gene signature activation in breast cancer in an absolute, single-patient manner Breast Cancer Res, 19, pp. 32. doi:10.1186/s13058-017-0824-7 (21 March 2017)
Lottrup G, Belling K, Leffers H, Nielsen JE, Dalgaard MD, Juul A, Skakkebæk NE, Brunak S, Rajpert-De Meyts E. Comparison of global gene expression profiles of microdissected human foetal Leydig cells with their normal and hyperplastic adult equivalents. Mol Hum Reprod, pp. 1-16. doi:10.1093/molehr/gax012 (17 March 2017)
Zheng X, Gogarten SM, Lawrence M, Stilp A, Conomos MP, Weir BS, Laurie C, Levine D. SeqArray - A storage-efficient high-performance data format for WGS variant calls. Bioinformatics. doi:10.1093/bioinformatics/btx145 (16 March 2017)
Foroushani A, Agrahari R, Docking R, Chang L, Duns G, Hudoba M, Karsan A, Zare H. Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications. BMC Med Genomics, 10(1), pp. 16. doi:10.1186/s12920-017-0253-6 (16 March 2017)
Srinivasan S, Di Dario M, Russo A, Menon R, Brini E, Romeo M, Sangalli F, Costa GD, Rodegher M, Radaelli M, Moiola L, Cantarella D, Medico E, Martino G, Furlan R, Martinelli V, Comi G, Farina C. Dysregulation of MS risk genes and pathways at distinct stages of disease Neurol Neuroimmunol Neuroinflamm, 4(3), pp. e337. doi:10.1212/NXI.0000000000000337 (16 March 2017)
Carlson MO, Gazave E, Gore MA, Smart CD. Temporal Genetic Dynamics of an Experimental, Biparental Field Population of Phytophthora capsici Front Genet, 8, pp. 26. doi:10.3389/fgene.2017.00026 (13 March 2017)
Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J. Estimating Gene Regulatory Networks with pandaR. Bioinformatics. doi:10.1093/bioinformatics/btx139 (11 March 2017)

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