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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


20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2016-06-30T20:40:08-04:00.

Almstrup K, Lindhardt Johansen M, Busch AS, Hagen CP, Nielsen JE, Petersen JH, Juul A. Pubertal development in healthy children is mirrored by DNA methylation patterns in peripheral blood Sci Rep, 6, pp. 28657. doi:10.1038/srep28657 (28 June 2016)
Kovi MR, Abdelhalim M, Kunapareddy A, Ergon Å, Tronsmo AM, Brurberg MB, Hofgaard IS, Asp T, Rognli OA. Global transcriptome changes in perennial ryegrass during early infection by pink snow mould Sci Rep, 6, pp. 28702. doi:10.1038/srep28702 (27 June 2016)
Grote S, Prüfer K, Kelso J, Dannemann M. ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain. Bioinformatics. doi:10.1093/bioinformatics/btw392 (26 June 2016)
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)
Ab Mutalib NS, Othman SN, Mohamad Yusof A, Abdullah Suhaimi SN, Muhammad R, Jamal R. Integrated microRNA, gene expression and transcription factors signature in papillary thyroid cancer with lymph node metastasis PeerJ, 4, pp. e2119. doi:10.7717/peerj.2119 (15 June 2016)
Robles EF, Mena-Varas M, Barrio L, Merino-Cortes SV, Balogh P, Du MQ, Akasaka T, Parker A, Roa S, Panizo C, Martin-Guerrero I, Siebert R, Segura V, Agirre X, Macri-Pellizeri L, Aldaz B, Vilas-Zornoza A, Zhang S, Moody S, Calasanz MJ, Tousseyn T, Broccardo C, Brousset P, Campos-Sanchez E, Cobaleda C, Sanchez-Garcia I, Fernandez-Luna JL, Garcia-Muñoz R, Pena E, Bellosillo B, Salar A, Baptista MJ, Hernandez-Rivas JM, Gonzalez M, Terol MJ, Climent J, Ferrandez A, Sagaert X, Melnick AM, Prosper F, Oscier DG, Carrasco YR, Dyer MJ, Martinez-Climent JA. Homeobox NKX2-3 promotes marginal-zone lymphomagenesis by activating B-cell receptor signalling and shaping lymphocyte dynamics Nat Commun, 7, pp. 11889. doi:10.1038/ncomms11889 (14 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)
Wu T, He K, Ang S, Ying J, Zhang S, Zhang T, Xue Y, Tang M. Impairments of spatial learning and memory following intrahippocampal injection in rats of 3-mercaptopropionic acid-modified CdTe quantum dots and molecular mechanisms Int J Nanomedicine, 11, pp. 2737-2755. doi:10.2147/IJN.S104985 (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)
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)


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