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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 2017-06-28T18:20:12-04:00.

Wilkinson S, Bishop SC, Allen AR, McBride SH, Skuce RA, Bermingham M, Woolliams JA, Glass EJ. Fine-mapping host genetic variation underlying outcomes to Mycobacterium bovis infection in dairy cows BMC Genomics, 18, pp. 477. doi:10.1186/s12864-017-3836-x (24 June 2017)

Liu H, Smith TP, Nonneman DJ, Dekkers JC, Tuggle CK. A high-quality annotated transcriptome of swine peripheral blood BMC Genomics, 18, pp. 479. doi:10.1186/s12864-017-3863-7 (24 June 2017)

Mateus A, Määttä TA, Savitski MM. Thermal proteome profiling: unbiased assessment of protein state through heat-induced stability changes Proteome Sci, 15, pp. 13. doi:10.1186/s12953-017-0122-4 (24 June 2017)

Tomar T, Alkema NG, Schreuder L, Meersma GJ, de Meyer T, van Criekinge W, Klip HG, Fiegl H, van Nieuwenhuysen E, Vergote I, Widschwendter M, Schuuring E, van der Zee AG, de Jong S, Wisman GB. Methylome analysis of extreme chemoresponsive patients identifies novel markers of platinum sensitivity in high-grade serous ovarian cancer BMC Med, 15, pp. 116. doi:10.1186/s12916-017-0870-0 (23 June 2017)

Frattini S, Capra E, Lazzari B, McKay SD, Coizet B, Talenti A, Groppetti D, Riccaboni P, Pecile A, Chessa S, Castiglioni B, Williams JL, Pagnacco G, Stella A, Crepaldi P. Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus BMC Genomics, 18, pp. 476. doi:10.1186/s12864-017-3866-4 (23 June 2017)

Landis JB, Soltis DE, Soltis PS. Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae) BMC Genomics, 18, pp. 475. doi:10.1186/s12864-017-3868-2 (23 June 2017)

Kordonowy L, MacManes M. Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent, Peromyscus eremicus BMC Genomics, 18, pp. 473. doi:10.1186/s12864-017-3840-1 (23 June 2017)

Rogers TD, Anacker AM, Kerr TM, Forsberg CG, Wang J, Zhang B, Veenstra-VanderWeele J. Effects of a social stimulus on gene expression in a mouse model of fragile X syndrome Mol Autism, 8, pp. 30. doi:10.1186/s13229-017-0148-6 (23 June 2017)

Lee S, Cassone BJ, Wijeratne A, Jun TH, Michel AP, Mian MA. Transcriptomic dynamics in soybean near-isogenic lines differing in alleles for an aphid resistance gene, following infestation by soybean aphid biotype 2 BMC Genomics, 18, pp. 472. doi:10.1186/s12864-017-3829-9 (23 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)

Landolt L, Eikrem Ø, Strauss P, Scherer A, Lovett DH, Beisland C, Finne K, Osman T, Ibrahim MM, Gausdal G, Ahmed L, Lorens JB, Thiery JP, Tan TZ, Sekulic M, Marti HP. Clear Cell Renal Cell Carcinoma is linked to Epithelial-to-Mesenchymal Transition and to Fibrosis. Physiol Rep, 5(11). doi:10.14814/phy2.13305 (10 June 2017)

Green R, Wilkins C, Thomas S, Sekine A, Hendrick DM, Voss K, Ireton RC, Mooney M, Go JT, Choonoo G, Jeng S, de Villena FP, Ferris MT, McWeeney S, Gale M Jr. Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross G3 (Bethesda), 7(6), pp. 1665-1682. doi:10.1534/g3.117.041624 (5 June 2017)

Gel B, Serra E. karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics. doi:10.1093/bioinformatics/btx346 (29 May 2017)

Mock A, Murphy S, Morris J, Marass F, Rosenfeld N, Massie C. CVE: an R package for interactive variant prioritisation in precision oncology. BMC Med Genomics, 10(1), pp. 37. doi:10.1186/s12920-017-0261-6 (25 May 2017)

Suomi T, Seyednasrollah F, Jaakkola MK, Faux T, Elo LL. ROTS: An R package for reproducibility-optimized statistical testing. PLoS Comput Biol, 13(5), pp. e1005562. doi:10.1371/journal.pcbi.1005562 (25 May 2017)

Städler N, Dondelinger F, Hill SM, Akbani R, Lu Y, Mills GB, Mukherjee S. Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study. Bioinformatics. doi:10.1093/bioinformatics/btx322 (23 May 2017)

Lågstad S, Zhao S, Hoff AM, Johannessen B, Christian Lingjærde O, Skotheim RI. chimeraviz: A tool for visualizing chimeric RNA. Bioinformatics. doi:10.1093/bioinformatics/btx329 (19 May 2017)