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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 2017-04-26T03:20:09-04:00.

Romney AL, Podrabsky JE. Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish, Austrofundulus limnaeus EvoDevo, 8, pp. 6. doi:10.1186/s13227-017-0069-7 (21 April 2017)
Ortiz JP, Revale S, Siena LA, Podio M, Delgado L, Stein J, Leblanc O, Pessino SC. A reference floral transcriptome of sexual and apomictic Paspalum notatum BMC Genomics, 18, pp. 318. doi:10.1186/s12864-017-3700-z (21 April 2017)
Diaz-Beltran L, Esteban FJ, Varma M, Ortuzk A, David M, Wall DP. Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes BMC Genomics, 18, pp. 315. doi:10.1186/s12864-017-3667-9 (20 April 2017)
Federico L, Chong Z, Zhang D, McGrail DJ, Zhao W, Jeong KJ, Vellano CP, Ju Z, Gagea M, Liu S, Mitra S, Dennison JB, Lorenzi PL, Cardnell R, Diao L, Wang J, Lu Y, Byers LA, Perou CM, Lin SY, Mills GB. A murine preclinical syngeneic transplantation model for breast cancer precision medicine Sci Adv, 3(4), pp. e1600957. doi:10.1126/sciadv.1600957 (19 April 2017)
Bennett BD, Bushel PR. goSTAG: gene ontology subtrees to tag and annotate genes within a set. Source Code Biol Med, 12, pp. 6. doi:10.1186/s13029-017-0066-1 (13 April 2017)
Pirkl M, Diekmann M, van der Wees M, Beerenwinkel N, Fröhlich H, Markowetz F. Inferring modulators of genetic interactions with epistatic nested effects models. PLoS Comput Biol, 13(4), pp. e1005496. doi:10.1371/journal.pcbi.1005496 (13 April 2017)
Naake T, Gaquerel E. MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data. Bioinformatics. doi:10.1093/bioinformatics/btx159 (11 April 2017)
Parodi AC, Sangalli LM, Vantini S, Amati B, Secchi P, Morelli MJ. FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes. Bioinformatics. doi:10.1093/bioinformatics/btx201 (7 April 2017)
Zhou X, Meng G, Nardini C, Mei H. Systemic Evaluation of Cellular Reprogramming Processes exploiting a novel R-tool: eegc. Bioinformatics. doi:10.1093/bioinformatics/btx205 (7 April 2017)
Mifsud B, Martincorena I, Darbo E, Sugar R, Schoenfelder S, Fraser P, Luscombe NM. GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data. PLoS One, 12(4), pp. e0174744. doi:10.1371/journal.pone.0174744 (5 April 2017)
Aleksandr I, He L, Aittokallio T, Tang J. SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinformatics. doi:10.1093/bioinformatics/btx162 (4 April 2017)
Aleksandr I, He L, Aittokallio T, Tang J. SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinformatics. doi:10.1093/bioinformatics/btx168 (4 April 2017)
Zhang JD, Hatje K, Sturm G, Broger C, Ebeling M, Burtin M, Terzi F, Pomposiello SI, Badi L. Detect tissue heterogeneity in gene expression data with BioQC. BMC Genomics, 18(1), pp. 277. doi:10.1186/s12864-017-3661-2 (4 April 2017)
Salih MA, Fakiola M, Lyons PA, Younis BM, Musa AM, Elhassan AM, Anderson D, Syn G, Ibrahim ME, Blackwell JM, Mohamed HS. Expression profiling of Sudanese visceral leishmaniasis patients pre- and post-treatment with sodium stibogluconate. Parasite Immunol. doi:10.1111/pim.12431 (31 March 2017)
Lim JH, Lee SY, Kim JH. TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data. Genomics Inform, 15(1), pp. 51-53. doi:10.5808/GI.2017.15.1.51 (29 March 2017)
Park SJ, Kim JH, Yoon BH, Kim SY. A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages. Genomics Inform, 15(1), pp. 11-18. doi:10.5808/GI.2017.15.1.11 (29 March 2017)
Cavalcante RG, Sartor MA. annotatr: Genomic regions in context. Bioinformatics. doi:10.1093/bioinformatics/btx183 (29 March 2017)
Zhang Z, Newton K, Kummerfeld SK, Webster J, Kirkpatrick DS, Phu L, Eastham-Anderson J, Liu J, Lee WP, Wu J, Li H, Junttila MR, Dixit VM. Transcription factor Etv5 is essential for the maintenance of alveolar type II cells Proc Natl Acad Sci U S A, 114(15), pp. 3903-3908. doi:10.1073/pnas.1621177114 (28 March 2017)
Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M. SC3: consensus clustering of single-cell RNA-seq data. Nat Methods. doi:10.1038/nmeth.4236 (27 March 2017)
Heim JB, Squirewell EJ, Neu A, Zocher G, Sominidi-Damodaran S, Wyles SP, Nikolova E, Behrendt N, Saunte DM, Lock-Andersen J, Gaonkar KS, Yan H, Sarkaria JN, Krendel M, van Deursen J, Sprangers R, Stehle T, Böttcher RT, Lee JH, Ordog T, Meves A. Myosin-1E interacts with FAK proline-rich region 1 to induce fibronectin-type matrix Proc Natl Acad Sci U S A, 114(15), pp. 3933-3938. doi:10.1073/pnas.1614894114 (27 March 2017)

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