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Ramos, M, et al. (2017) Software for the Integration of Multiomics Experiments in Bioconductor Cancer Research 77:e39-e42. doi:10.1158/0008-5472.CAN-17-0344
Pasolli, E, et al. (2017) Accessible, curated metagenomic data through ExperimentHub Nature Methods 14, 1023–1024. doi:10.1038/nmeth.4468
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).
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
Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2019-01-22T23:40:06-05:00.

Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A. Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection. Sci Rep, 9(1), pp. 213. doi:10.1038/s41598-018-36135-3 (18 January 2019)
Singh A, Shannon CP, Gautier B, Rohart F, Vacher M, Tebbutt SJ, Lê Cao KA. DIABLO: an integrative approach for identifying key molecular drivers from multi-omic assays. Bioinformatics. doi:10.1093/bioinformatics/bty1054 (18 January 2019)
Nash T, Huff M, Glen WB Jr, Hardiman G. Pipeline for Integrated Microarray Expression Normalization Tool Kit (PIMENTo) for Tumor Microarray Profiling Experiments. Methods Mol Biol, 1908, pp. 153-168. doi:10.1007/978-1-4939-9004-7_11 (17 January 2019)
Orzechowski P, Moore JH. EBIC: an open source software for high-dimensional and big data analyses. Bioinformatics. doi:10.1093/bioinformatics/btz027 (14 January 2019)
Griffith JC, Morgan XC. Invited Commentary: Improving accessibility of the Human Microbiome Project data through integration with R/Bioconductor. Am J Epidemiol. doi:10.1093/aje/kwz007 (10 January 2019)
Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L. HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor. Am J Epidemiol. doi:10.1093/aje/kwz006 (10 January 2019)
Kort EJ, Jovinge S. Streamlined analysis of LINCS L1000 data with the slinky package for R. Bioinformatics. doi:10.1093/bioinformatics/btz002 (10 January 2019)
Morais DAA, Almeida RMC, Dalmolin RJS. transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein-protein interaction. Bioinformatics. doi:10.1093/bioinformatics/btz007 (8 January 2019)
Fuentes N, Silveyra P. Lung microRNA Profiling Across the Estrous Cycle in Ozone-exposed Mice. J Vis Exp(143). doi:10.3791/58664 (7 January 2019)
Kucukural A, Yukselen O, Ozata DM, Moore MJ, Garber M. DEBrowser: interactive differential expression analysis and visualization tool for count data. BMC Genomics, 20(1), pp. 6. doi:10.1186/s12864-018-5362-x (5 January 2019)
Lee S, Cook D, Lawrence M. plyranges: a grammar of genomic data transformation. Genome Biol, 20(1), pp. 4. doi:10.1186/s13059-018-1597-8 (4 January 2019)
Xu T, Su N, Liu L, Zhang J, Wang H, Zhang W, Gui J, Yu K, Li J, Le TD. miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase. BMC Bioinformatics, 19(Suppl 19), pp. 514. doi:10.1186/s12859-018-2531-5 (31 December 2018)
Poell JB, Mendeville M, Sie D, Brink A, Brakenhoff RH, Ylstra B. ACE: Absolute Copy number Estimation from low-coverage whole-genome sequencing data. Bioinformatics. doi:10.1093/bioinformatics/bty1055 (28 December 2018)
Picart-Armada S, Fernández-Albert F, Vinaixa M, Yanes O, Perera-Lluna A. FELLA: an R package to enrich metabolomics data. BMC Bioinformatics, 19(1), pp. 538. doi:10.1186/s12859-018-2487-5 (22 December 2018)
Ge SX, Son EW, Yao R. iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. BMC Bioinformatics, 19(1), pp. 534. doi:10.1186/s12859-018-2486-6 (19 December 2018)
Francis M, Grider A. MiRNA-target interactions in osteogenic signaling pathways involving zinc via the metal regulatory element. Biometals. doi:10.1007/s10534-018-00162-4 (18 December 2018)
Böttcher C, Schlickeiser S, Sneeboer MAM, Kunkel D, Knop A, Paza E, Fidzinski P, Kraus L, Snijders GJL, Kahn RS, Schulz AR, Mei HE, Hol EM, Siegmund B, Glauben R, Spruth EJ, de Witte LD, Priller J. Human microglia regional heterogeneity and phenotypes determined by multiplexed single-cell mass cytometry. Nat Neurosci, 22(1), pp. 78-90. doi:10.1038/s41593-018-0290-2 (17 December 2018)
Heinrich P, Kohler C, Ellmann L, Kuerner P, Spang R, Oefner PJ, Dettmer K. Correcting for natural isotope abundance and tracer impurity in MS-, MS/MS- and high-resolution-multiple-tracer-data from stable isotope labeling experiments with IsoCorrectoR. Sci Rep, 8(1), pp. 17910. doi:10.1038/s41598-018-36293-4 (17 December 2018)
Boca SM, Leek JT. A direct approach to estimating false discovery rates conditional on covariates. PeerJ, 6, pp. e6035. doi:10.7717/peerj.6035 (10 December 2018)

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