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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 2017-10-20T01:20:08-04:00.

Lawrence M, Gentleman R. VariantTools: an extensible framework for developing and testing variant callers. Bioinformatics, 33(20), pp. 3311-3313. doi:10.1093/bioinformatics/btx450 (15 October 2017)
de Santiago I, Carroll T. Analysis of ChIP-seq Data in R/Bioconductor. Methods Mol Biol, 1689, pp. 195-226. doi:10.1007/978-1-4939-7380-4_17 (14 October 2017)
Roost MS, Slieker RC, Bialecka M, van Iperen L, Gomes Fernandes MM, He N, Suchiman HE, Szuhai K, Carlotti F, de Koning EJ, Mummery CL, Heijmans BT, Chuva de Sousa Lopes SM. DNA methylation and transcriptional trajectories during human development and reprogramming of isogenic pluripotent stem cells Nat Commun, 8, pp. 908. doi:10.1038/s41467-017-01077-3 (13 October 2017)
Fang F, Pan J, Li Y, Li Y, Feng X, Wang J. Identification of potential transcriptomic markers in developing asthma: An integrative analysis of gene expression profiles. Mol Immunol, 92, pp. 38-44. doi:10.1016/j.molimm.2017.09.021 (12 October 2017)
Ye Y, Zhang R, Zheng W, Liu S, Zhou F. RIFS: a randomly restarted incremental feature selection algorithm Sci Rep, 7, pp. 13013. doi:10.1038/s41598-017-13259-6 (12 October 2017)
Béguelin W, Rivas MA, Calvo Fernández MT, Teater M, Purwada A, Redmond D, Shen H, Challman MF, Elemento O, Singh A, Melnick AM. EZH2 enables germinal centre formation through epigenetic silencing of CDKN1A and an Rb-E2F1 feedback loop Nat Commun, 8, pp. 877. doi:10.1038/s41467-017-01029-x (12 October 2017)
Jiang X, Zhang H, Duan F, Quan X. Identify Huntington’s disease associated genes based on restricted Boltzmann machine with RNA-seq data BMC Bioinformatics, 18, pp. 447. doi:10.1186/s12859-017-1859-6 (11 October 2017)
Silva-Marrero JI, Sáez A, Caballero-Solares A, Viegas I, Almajano MP, Fernández F, Baanante IV, Metón I. A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata) BMC Genomics, 18, pp. 768. doi:10.1186/s12864-017-4148-x (11 October 2017)
Lombardo F, Salvemini M, Fiorillo C, Nolan T, Zwiebel LJ, Ribeiro JM, Arcà B. Deciphering the olfactory repertoire of the tiger mosquito Aedes albopictus BMC Genomics, 18, pp. 770. doi:10.1186/s12864-017-4144-1 (11 October 2017)
Wai CM, Zhang J, Jones TC, Nagai C, Ming R. Cell wall metabolism and hexose allocation contribute to biomass accumulation in high yielding extreme segregants of a Saccharum interspecific F2 population BMC Genomics, 18, pp. 773. doi:10.1186/s12864-017-4158-8 (11 October 2017)
Pourteymour S, Hjorth M, Lee S, Holen T, Langleite TM, Jensen J, Birkeland KI, Drevon CA, Eckardt K. Dual specificity phosphatase 5 and 6 are oppositely regulated in human skeletal muscle by acute exercise Physiol Rep, 5(19), pp. e13459. doi:10.14814/phy2.13459 (9 October 2017)
Sun S, Xuan F, Ge X, Zhu J, Zhang W. Dynamic mRNA and miRNA expression analysis in response to hypoxia and reoxygenation in the blunt snout bream (Megalobrama amblycephala) Sci Rep, 7, pp. 12846. doi:10.1038/s41598-017-12537-7 (9 October 2017)
Takiuchi Y, Kobayashi M, Tada K, Iwai F, Sakurada M, Hirabayashi S, Nagata K, Shirakawa K, Shindo K, Yasunaga JI, Murakawa Y, Rajapakse V, Pommier Y, Matsuoka M, Takaori-Kondo A. HTLV-1 bZIP factor suppresses TDP1 expression through inhibition of NRF-1 in adult T-cell leukemia Sci Rep, 7, pp. 12849. doi:10.1038/s41598-017-12924-0 (9 October 2017)
Picart-Armada S, Thompson WK, Buil A, Perera-Lluna A. An R package to compute diffusion-based scores on biological networks: diffuStats. Bioinformatics. doi:10.1093/bioinformatics/btx632 (5 October 2017)
Li Y, Xia Y, Han M, Chen G, Zhang D, Thasler WE, Protzer U, Ning Q. IFN-α-mediated Base Excision Repair Pathway Correlates with Antiviral Response Against Hepatitis B Virus Infection Sci Rep, 7, pp. 12715. doi:10.1038/s41598-017-13082-z (5 October 2017)
Liu Y, Wu P, Zhou J, Johnson-Pais TL, Lai Z, Chowdhury WH, Rodriguez R, Chen Y. XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation. BMC Bioinformatics, 18(Suppl 11), pp. 384. doi:10.1186/s12859-017-1803-9 (3 October 2017)
Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane AR, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics, 18(1), pp. 437. doi:10.1186/s12859-017-1847-x (3 October 2017)
Hung LH, Shi K, Wu M, Young WC, Raftery AE, Yeung KY. fastBMA: scalable network inference and transitive reduction. Gigascience, 6(10), pp. 1-10. doi:10.1093/gigascience/gix078 (1 October 2017)
Serviss JT, Gådin JR, Eriksson P, Folkersen L, Grandér D. ClusterSignificance: a bioconductor package facilitating statistical analysis of class cluster separations in dimensionality reduced data. Bioinformatics, 33(19), pp. 3126-3128. doi:10.1093/bioinformatics/btx393 (1 October 2017)
Lareau CA, Aryee MJ. diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data. Bioinformatics. doi:10.1093/bioinformatics/btx623 (29 September 2017)

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