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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 2016-09-24T19:00:18-04:00.

Chen H, Lau MC, Wong MT, Newell EW, Poidinger M, Chen J. Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline. PLoS Comput Biol, 12(9), pp. e1005112. doi:10.1371/journal.pcbi.1005112 (23 September 2016)
Liu P, Jiang W, Zhou S, Gao J, Zhang H. Combined Analysis of ChIP Sequencing and Gene Expression Dataset in Breast Cancer. Pathol Oncol Res. doi:10.1007/s12253-016-0116-z (21 September 2016)
H Backman TW, Girke T. systemPipeR: NGS workflow and report generation environment. BMC Bioinformatics, 17, pp. 388. doi:10.1186/s12859-016-1241-0 (20 September 2016)
Bermick JR, Lambrecht NJ, denDekker AD, Kunkel SL, Lukacs NW, Hogaboam CM, Schaller MA. Neonatal monocytes exhibit a unique histone modification landscape Clin Epigenetics, 8, pp. 99. doi:10.1186/s13148-016-0265-7 (20 September 2016)
Toropainen S, Niskanen EA, Malinen M, Sutinen P, Kaikkonen MU, Palvimo JJ. Global analysis of transcription in castration-resistant prostate cancer cells uncovers active enhancers and direct androgen receptor targets Sci Rep, 6, pp. 33510. doi:10.1038/srep33510 (19 September 2016)
Wang X, Zhang L, Li H, Sun W, Zhang H, Lai M. THBS2 is a Potential Prognostic Biomarker in Colorectal Cancer Sci Rep, 6, pp. 33366. doi:10.1038/srep33366 (16 September 2016)
Cao Z, Zhang S. An integrative and comparative study of pan-cancer transcriptomes reveals distinct cancer common and specific signatures Sci Rep, 6, pp. 33398. doi:10.1038/srep33398 (16 September 2016)
Sen S, Block KF, Pasini A, Baylin SB, Easwaran H. Genome-wide positioning of bivalent mononucleosomes BMC Med Genomics, 9, pp. 60. doi:10.1186/s12920-016-0221-6 (15 September 2016)
Müller L, Gerighausen D, Farman M, Zeckzer D. Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering BMC Bioinformatics, 17, pp. 377. doi:10.1186/s12859-016-1248-6 (15 September 2016)
Käser-Pébernard S, Pfefferli C, Aschinger C, Wicky C. Fine-tuning of chromatin composition and Polycomb recruitment by two Mi2 homologues during C. elegans early embryonic development Epigenetics Chromatin, 9, pp. 39. doi:10.1186/s13072-016-0091-3 (15 September 2016)
Dheilly E, Gall SL, Guillou MC, Renou JP, Bonnin E, Orsel M, Lahaye M. Cell wall dynamics during apple development and storage involves hemicellulose modifications and related expressed genes BMC Plant Biol, 16, pp. 201. doi:10.1186/s12870-016-0887-0 (15 September 2016)
Zheng J, Harris MR, Masci AM, Lin Y, Hero A, Smith B, He Y. The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis J Biomed Semantics, 7, pp. 53. doi:10.1186/s13326-016-0100-2 (14 September 2016)
duVerle DA, Yotsukura S, Nomura S, Aburatani H, Tsuda K. CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. BMC Bioinformatics, 17(1), pp. 363. doi:10.1186/s12859-016-1175-6 (13 September 2016)
Gupta R, Forloni M, Bisserier M, Dogra SK, Yang Q, Wajapeyee N. Interferon alpha-inducible protein 6 regulates NRASQ61K-induced melanomagenesis and growth eLife, 5, pp. e16432. doi:10.7554/eLife.16432 (8 September 2016)
Roberti A, Dobay MP, Bisig B, Vallois D, Boéchat C, Lanitis E, Bouchindhomme B, Parrens MC, Bossard C, Quintanilla-Martinez L, Missiaglia E, Gaulard P, de Leval L. Type II enteropathy-associated T-cell lymphoma features a unique genomic profile with highly recurrent SETD2 alterations Nat Commun, 7, pp. 12602. doi:10.1038/ncomms12602 (7 September 2016)
Wieczorek S, Combes F, Lazar C, Giai Gianetto Q, Gatto L, Dorffer A, Hesse AM, Coute Y, Ferro M, Bruley C, Burger T. DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics. Bioinformatics. doi:10.1093/bioinformatics/btw580 (6 September 2016)
Poole W, Gibbs DL, Shmulevich I, Bernard B, Knijnenburg TA. Combining dependent P-values with an empirical adaptation of Brown's method. Bioinformatics, 32(17), pp. i430-i436. doi:10.1093/bioinformatics/btw438 (1 September 2016)
Oytam Y, Sobhanmanesh F, Duesing K, Bowden JC, Osmond-McLeod M, Ross J. Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets. BMC Bioinformatics, 17(1), pp. 332. doi:10.1186/s12859-016-1212-5 (1 September 2016)
Azad A, Rajwa B, Pothen A. Immunophenotype Discovery, Hierarchical Organization, and Template-Based Classification of Flow Cytometry Samples. Front Oncol, 6, pp. 188. doi:10.3389/fonc.2016.00188 (31 August 2016)
Zollars E, Courtney SM, Wolf BJ, Allaire N, Ranger A, Hardiman G, Petri M. Clinical Application of a Modular Genomics Technique in Systemic Lupus Erythematosus: Progress towards Precision Medicine Int J Genomics, 2016, pp. 7862962. doi:10.1155/2016/7862962 (30 August 2016)

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