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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 2017-08-19T09:20:10-04:00.

Duan N, Bai Y, Sun H, Wang N, Ma Y, Li M, Wang X, Jiao C, Legall N, Mao L, Wan S, Wang K, He T, Feng S, Zhang Z, Mao Z, Shen X, Chen X, Jiang Y, Wu S, Yin C, Ge S, Yang L, Jiang S, Xu H, Liu J, Wang D, Qu C, Wang Y, Zuo W, Xiang L, Liu C, Zhang D, Gao Y, Xu Y, Xu K, Chao T, Fazio G, Shu H, Zhong GY, Cheng L, Fei Z, Chen X. Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement Nat Commun, 8, pp. 249. doi:10.1038/s41467-017-00336-7 (15 August 2017)
Li S, Christiansen L, Christensen K, Kruse TA, Redmond P, Marioni RE, Deary IJ, Tan Q. Identification, replication and characterization of epigenetic remodelling in the aging genome: a cross population analysis Sci Rep, 7, pp. 8183. doi:10.1038/s41598-017-08346-7 (15 August 2017)
Beauvais-Flück R, Slaveykova VI, Cosio C. Cellular toxicity pathways of inorganic and methyl mercury in the green microalga Chlamydomonas reinhardtii Sci Rep, 7, pp. 8034. doi:10.1038/s41598-017-08515-8 (14 August 2017)
Shi YX, Yin JY, Shen Y, Zhang W, Zhou HH, Liu ZQ. Genome-scale analysis identifies NEK2, DLGAP5 and ECT2 as promising diagnostic and prognostic biomarkers in human lung cancer Sci Rep, 7, pp. 8072. doi:10.1038/s41598-017-08615-5 (14 August 2017)
Hanouna G, Mesnard L, Vandermeersch S, Perez J, Placier S, Haymann JP, Campagne F, Moroch J, Bataille A, Baud L, Letavernier E. Specific calpain inhibition protects kidney against inflammaging Sci Rep, 7, pp. 8016. doi:10.1038/s41598-017-07922-1 (14 August 2017)
Dercle L, Ammari S, Bateson M, Durand PB, Haspinger E, Massard C, Jaudet C, Varga A, Deutsch E, Soria JC, Ferté C. Limits of radiomic-based entropy as a surrogate of tumor heterogeneity: ROI-area, acquisition protocol and tissue site exert substantial influence Sci Rep, 7, pp. 7952. doi:10.1038/s41598-017-08310-5 (11 August 2017)
Li Y, Ding X, Wang X, He T, Zhang H, Yang L, Wang T, Chen L, Gai J, Yang S. Genome-wide comparative analysis of DNA methylation between soybean cytoplasmic male-sterile line NJCMS5A and its maintainer NJCMS5B BMC Genomics, 18, pp. 596. doi:10.1186/s12864-017-3962-5 (10 August 2017)
de Castro MH, de Klerk D, Pienaar R, Rees DJ, Mans BJ. Sialotranscriptomics of Rhipicephalus zambeziensis reveals intricate expression profiles of secretory proteins and suggests tight temporal transcriptional regulation during blood-feeding Parasit Vectors, 10, pp. 384. doi:10.1186/s13071-017-2312-4 (10 August 2017)
Zhang Q, Zeng LP, Zhou P, Irving AT, Li S, Shi ZL, Wang LF. IFNAR2-dependent gene expression profile induced by IFN-α in Pteropus alecto bat cells and impact of IFNAR2 knockout on virus infection PLoS One, 12(8), pp. e0182866. doi:10.1371/journal.pone.0182866 (9 August 2017)
Zheng T, Wang A, Hu D, Wang Y. Molecular mechanisms of breast cancer metastasis by gene expression profile analysis. Mol Med Rep. doi:10.3892/mmr.2017.7157 (3 August 2017)
Thierion E, Le Men J, Collombet S, Hernandez C, Coulpier F, Torbey P, Thomas-Chollier M, Noordermeer D, Charnay P, Gilardi-Hebenstreit P. Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements PLoS Genet, 13(7), pp. e1006903. doi:10.1371/journal.pgen.1006903 (27 July 2017)
Jia G, Wang X, Xiao G. A permutation-based non-parametric analysis of CRISPR screen data BMC Genomics, 18, pp. 545. doi:10.1186/s12864-017-3938-5 (19 July 2017)
Rodríguez-García A, Sola-Landa A, Barreiro C. RNA-Seq-Based Comparative Transcriptomics: RNA Preparation and Bioinformatics. Methods Mol Biol, 1645, pp. 59-72. doi:10.1007/978-1-4939-7183-1_5 (16 July 2017)
Saxena A, Sachin K, Bhatia AK. System Level Meta-analysis of Microarray Datasets for Elucidation of Diabetes Mellitus Pathobiology. Curr Genomics, 18(3), pp. 298-304. doi:10.2174/1389202918666170105093339 (1 July 2017)
Bradley G, Barrett SJ. CausalR - extracting mechanistic sense from genome scale data. Bioinformatics. doi:10.1093/bioinformatics/btx425 (29 June 2017)
Bemis KA, Vitek O. matter: an R package for rapid prototyping with larger-than-memory datasets on disk. Bioinformatics. doi:10.1093/bioinformatics/btx392 (15 June 2017)
Patil SU, Calatroni A, Schneider M, Steinbrecher J, Smith N, Washburn C, Ma A, Shreffler WG. Data-driven programmatic approach to analysis of basophil activation tests. Cytometry B Clin Cytom. doi:10.1002/cyto.b.21537 (15 June 2017)
Drummond MJ, Reidy PT, Baird LM, Dalley BK, Howard MT. Leucine Differentially Regulates Gene-Specific Translation in Mouse Skeletal Muscle. J Nutr. doi:10.3945/jn.117.251181 (14 June 2017)
Xu T, Duy Le T, Liu L, Su N, Wang R, Sun B, Colaprico A, Bontempi G, Li J. CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation, and visualization. Bioinformatics. doi:10.1093/bioinformatics/btx378 (12 June 2017)

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