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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 2017-02-21T09:20:10-05:00.

Coda DM, Gaarenstroom T, East P, Patel H, Miller DS, Lobley A, Matthews N, Stewart A, Hill CS. Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling eLife, 6, pp. e22474. doi:10.7554/eLife.22474 (13 February 2017)
Duffy DJ, Krstic A, Halasz M, Schwarzl T, Konietzny A, Iljin K, Higgins DG, Kolch W. Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance Genome Med, 9, pp. 15. doi:10.1186/s13073-017-0407-3 (10 February 2017)
Chow YP, Alias H, Jamal R. Meta-analysis of gene expression in relapsed childhood B-acute lymphoblastic leukemia BMC Cancer, 17, pp. 120. doi:10.1186/s12885-017-3103-1 (10 February 2017)
Pintarelli G, Cotroneo CE, Noci S, Dugo M, Galvan A, Delli Carpini S, Citterio L, Manunta P, Incarbone M, Tosi D, Santambrogio L, Dragani TA, Colombo F. Genetic susceptibility variants for lung cancer: replication study and assessment as expression quantitative trait loci Sci Rep, 7, pp. 42185. doi:10.1038/srep42185 (9 February 2017)
Oczko-Wojciechowska M, Swierniak M, Krajewska J, Kowalska M, Kowal M, Stokowy T, Wojtas B, Rusinek D, Pawlaczek A, Czarniecka A, Szpak-Ulczok S, Gawlik T, Chmielik E, Tyszkiewicz T, Nikiel B, Lange D, Jarzab M, Wiench M, Jarzab B. Differences in the transcriptome of medullary thyroid cancer regarding the status and type of RET gene mutations Sci Rep, 7, pp. 42074. doi:10.1038/srep42074 (9 February 2017)
Picarda E, Bézie S, Boucault L, Autrusseau E, Kilens S, Meistermann D, Martinet B, Daguin V, Donnart A, Charpentier E, David L, Anegon I, Guillonneau C. Transient antibody targeting of CD45RC induces transplant tolerance and potent antigen-specific regulatory T cells JCI Insight, 2(3), pp. e90088. doi:10.1172/jci.insight.90088 (9 February 2017)
Bragg RM, Coffey SR, Weston RM, Ament SA, Cantle JP, Minnig S, Funk CC, Shuttleworth DD, Woods EL, Sullivan BR, Jones L, Glickenhaus A, Anderson JS, Anderson MD, Dunnett SB, Wheeler VC, MacDonald ME, Brooks SP, Price ND, Carroll JB. Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.HttQ111/+ model of Huntington’s disease Sci Rep, 7, pp. 41570. doi:10.1038/srep41570 (8 February 2017)
Parks DR, El Khettabi F, Chase E, Hoffman RA, Perfetto SP, Spidlen J, Wood JC, Moore WA, Brinkman RR. Evaluating flow cytometer performance with weighted quadratic least squares analysis of LED and multi-level bead data. Cytometry A. doi:10.1002/cyto.a.23052 (3 February 2017)
Quiroz-Zárate A, Harshfield BJ, Hu R, Knoblauch N, Beck AH, Hankinson SE, Carey V, Tamimi RM, Hunter DJ, Quackenbush J, Hazra A. Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue. PLoS One, 12(2), pp. e0170181. doi:10.1371/journal.pone.0170181 (2 February 2017)
Afroz S, Giddaluru J, Vishwakarma S, Naz S, Khan AA, Khan N. A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients Front Immunol, 8, pp. 74. doi:10.3389/fimmu.2017.00074 (2 February 2017)
Albarracin L, Kobayashi H, Iida H, Sato N, Nochi T, Aso H, Salva S, Alvarez S, Kitazawa H, Villena J. Transcriptomic Analysis of the Innate Antiviral Immune Response in Porcine Intestinal Epithelial Cells: Influence of Immunobiotic Lactobacilli Front Immunol, 8, pp. 57. doi:10.3389/fimmu.2017.00057 (2 February 2017)
Zhang Y, Xie J, Yang J, Fennell A, Zhang C, Ma Q. QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data. Bioinformatics, 33(3), pp. 450-452. doi:10.1093/bioinformatics/btw635 (1 February 2017)
Lecourieux F, Kappel C, Pieri P, Charon J, Pillet J, Hilbert G, Renaud C, Gomès E, Delrot S, Lecourieux D. Dissecting the Biochemical and Transcriptomic Effects of a Locally Applied Heat Treatment on Developing Cabernet Sauvignon Grape Berries Front Plant Sci, 8, pp. 53. doi:10.3389/fpls.2017.00053 (31 January 2017)
Cava C, Colaprico A, Bertoli G, Graudenzi A, Silva TC, Olsen C, Noushmehr H, Bontempi G, Mauri G, Castiglioni I. SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data. Int J Mol Sci, 18(2). doi:10.3390/ijms18020274 (27 January 2017)
Wong T, Deveson IW, Hardwick SA, Mercer TR. ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing. Bioinformatics. doi:10.1093/bioinformatics/btx038 (27 January 2017)
Rahmatallah Y, Zybailov B, Emmert-Streib F, Glazko G. GSAR: Bioconductor package for Gene Set analysis in R. BMC Bioinformatics, 18(1), pp. 61. doi:10.1186/s12859-017-1482-6 (24 January 2017)
Sato R, Nakano T, Hosonaga M, Sampetrean O, Harigai R, Sasaki T, Koya I, Okano H, Kudoh J, Saya H, Arima Y. RNA Sequencing Analysis Reveals Interactions between Breast Cancer or Melanoma Cells and the Tissue Microenvironment during Brain Metastasis Biomed Res Int, 2017, pp. 8032910. doi:10.1155/2017/8032910 (22 January 2017)
Wijetunga NA, Johnston AD, Maekawa R, Delahaye F, Ulahannan N, Kim K, Greally JM. SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. BMC Bioinformatics, 18(1), pp. 41. doi:10.1186/s12859-017-1477-3 (18 January 2017)

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