Publications

Bioconductor F1000 Research Channel launched!

Featured

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 2016-06-28T20:00:22-04:00.

Liu J, Siegmund KD. An evaluation of processing methods for HumanMethylation450 BeadChip data BMC Genomics, 17, pp. 469. doi:10.1186/s12864-016-2819-7 (22 June 2016)
Garcia-Garcia F, Panadero J, Dopazo J, Montaner D. Integrated Gene Set Analysis for microRNA Studies. Bioinformatics. doi:10.1093/bioinformatics/btw334 (20 June 2016)
Wen B, Xu S, Zhou R, Zhang B, Wang X, Liu X, Xu X, Liu S. PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq. BMC Bioinformatics, 17(1), pp. 244. doi:10.1186/s12859-016-1133-3 (17 June 2016)
Bain CC, Hawley CA, Garner H, Scott CL, Schridde A, Steers NJ, Mack M, Joshi A, Guilliams M, Mowat AM, Geissmann F, Jenkins SJ. Long-lived self-renewing bone marrow-derived macrophages displace embryo-derived cells to inhabit adult serous cavities Nat Commun, 7, pp. ncomms11852. doi:10.1038/ncomms11852 (13 June 2016)
Stokowy T, Garbulowski M, Fiskerstrand T, Holdhus R, Labun K, Sztromwasser P, Gilissen C, Hoischen A, Houge G, Petersen K, Jonassen I, Steen VM. RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data. Bioinformatics. doi:10.1093/bioinformatics/btw359 (10 June 2016)
Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL, Griffith M. GenVisR: Genomic Visualizations in R. Bioinformatics. doi:10.1093/bioinformatics/btw325 (10 June 2016)
Popa A, Lebrigand K, Paquet A, Nottet N, Robbe-Sermesant K, Waldmann R, Barbry P. RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing. F1000Res, 5, pp. 1309. doi:10.12688/f1000research.8964.1 (9 June 2016)
Nandal UK, van Kampen AH, Moerland PD. compendiumdb: an R package for retrieval and storage of functional genomics data. Bioinformatics. doi:10.1093/bioinformatics/btw335 (9 June 2016)
Maksimovic J, Phipson B, Oshlack A. A cross-package Bioconductor workflow for analysing methylation array data. F1000Res, 5, pp. 1281. doi:10.12688/f1000research.8839.1 (8 June 2016)
Estill MS, Bolnick JM, Waterland RA, Bolnick AD, Diamond MP, Krawetz SA. Assisted reproductive technology alters deoxyribonucleic acid methylation profiles in bloodspots of newborn infants. Fertil Steril. doi:10.1016/j.fertnstert.2016.05.006 (8 June 2016)
Ruhland MK, Loza AJ, Capietto AH, Luo X, Knolhoff BL, Flanagan KC, Belt BA, Alspach E, Leahy K, Luo J, Schaffer A, Edwards JR, Longmore G, Faccio R, DeNardo DG, Stewart SA. Stromal senescence establishes an immunosuppressive microenvironment that drives tumorigenesis Nat Commun, 7, pp. 11762. doi:10.1038/ncomms11762 (8 June 2016)
Touloumis A, Marioni JC, Tavaré S. HDTD: analyzing multi-tissue gene expression data. Bioinformatics. doi:10.1093/bioinformatics/btw224 (7 June 2016)
Miles S, Croxford MW, Abeysinghe AP, Breeden LL. Msa1 and Msa2 Modulate G1-Specific Transcription to Promote G1 Arrest and the Transition to Quiescence in Budding Yeast PLoS Genet, 12(6), pp. e1006088. doi:10.1371/journal.pgen.1006088 (6 June 2016)
Morota G, Beissinger TM, Peñagaricano F. MeSH-Informed Enrichment Analysis and MeSH-Guided Semantic Similarity among Functional Terms and Gene Products in Chicken. G3 (Bethesda). doi:10.1534/g3.116.031096 (3 June 2016)
Urdinguio RG, Torró MI, Bayón GF, Álvarez-Pitti J, Fernández AF, Redon P, Fraga MF, Lurbe E. Longitudinal study of DNA methylation during the first 5 years of life. J Transl Med, 14(1), pp. 160. doi:10.1186/s12967-016-0913-x (3 June 2016)
Hartley SW, Mullikin JC. Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq. Nucleic Acids Res. doi:10.1093/nar/gkw501 (1 June 2016)
Rao R, Yang Q, Orman MA, Berthiaume F, Ierapetritou MG, Androulakis IP. Burn trauma disrupts circadian rhythms in rat liver Int J Burns Trauma, 6(2), pp. 12-25. doi: (1 June 2016)
Ignatiadis N, Klaus B, Zaugg JB, Huber W. Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nat Methods. doi:10.1038/nmeth.3885 (30 May 2016)
Jia Z, Liu Y, Guan N, Bo X, Luo Z, Barnes MR. Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery. BMC Genomics, 17(1), pp. 414. doi:10.1186/s12864-016-2737-8 (27 May 2016)
Chung HR, Xu C, Fuchs A, Mund A, Lange M, Staege H, Schubert T, Bian C, Dunkel I, Eberharter A, Regnard C, Klinker H, Meierhofer D, Cozzuto L, Winterpacht A, Di Croce L, Min J, Will H, Kinkley S. PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3 eLife, 5, pp. e10607. doi:10.7554/eLife.10607 (25 May 2016)

Books

Monograph     R Programming for Bioinformatics     Bioconductor Case Studies

Book Chapters

Technical Reports and Working Papers

Compendia

Literature Search »

 

Courses & Conferences »

Bioconductor courses and conferences explore R programming and the analysis of genomic data. View catalog of a recent course material.

Packages »

Bioconductor's stable, semi-annual release:

Bioconductor is also available via Docker and Amazon Machine Images.