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Amezquita, R.A., Lun, A.T.L., Becht, E. et al. Orchestrating single-cell analysis with Bioconductor. Nature Methods (2019) doi:10.1038/s41592-019-0654-x

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 2020-01-24T03:00:06-05:00.

Yu G. Gene Ontology Semantic Similarity Analysis Using GOSemSim. Methods Mol Biol, 2117, pp. 207-215. doi:10.1007/978-1-0716-0301-7_11 (22 January 2020)

Galeota E, Kishore K, Pelizzola M. Ontology-driven integrative analysis of omics data through Onassis. Sci Rep, 10(1), pp. 703. doi:10.1038/s41598-020-57716-1 (20 January 2020)

Wu CT, Wang Y, Wang Y, Ebbels T, Karaman I, Graça G, Pinto R, Herrington DM, Wang Y, Yu G. Targeted Realignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection. Bioinformatics. doi:10.1093/bioinformatics/btaa037 (17 January 2020)

Kupcova Skalnikova H, Vodickova Kepkova K, Vodicka P. Luminex xMAP Assay to Quantify Cytokines in Cancer Patient Serum. Methods Mol Biol, 2108, pp. 65-88. doi:10.1007/978-1-0716-0247-8_6 (16 January 2020)

Maros ME, Capper D, Jones DTW, Hovestadt V, von Deimling A, Pfister SM, Benner A, Zucknick M, Sill M. Machine learning workflows to estimate class probabilities for precision cancer diagnostics on DNA methylation microarray data. Nat Protoc. doi:10.1038/s41596-019-0251-6 (13 January 2020)

Lv Y, He XY, Li D, Liu T, Wen GQ, Li J. Sex-specific and opposite modulatory aspects revealed by PPI network and pathway analysis of ischemic stroke in humans. PLoS One, 15(1), pp. e0227481. doi:10.1371/journal.pone.0227481 (3 January 2020)

He R, Ou S, Chen S, Ding S. Network Pharmacology-Based Study on the Molecular Biological Mechanism of Action for Compound Kushen Injection in Anti-Cancer Effect. Med Sci Monit, 26, pp. e918520. doi:10.12659/MSM.918520 (1 January 2020)

Sen K, Gadkari R, Agarwal R, Sundaram S. Differential DNA Methylation Patterns in Patients with Epilepsy due to Malformations of Cortical Development: A Pilot Study. Neurol India, 67(6), pp. 1469-1471. doi:10.4103/0028-3886.273638 (21 December 2019)

Li Y, Bian Y, Wang K, Wan XP. POLE mutations improve the prognosis of endometrial cancer via regulating cellular metabolism through AMF/AMFR signal transduction. BMC Med Genet, 20(1), pp. 202. doi:10.1186/s12881-019-0936-2 (21 December 2019)

LaBarre BA, Goncearenco A, Petrykowska HM, Jaratlerdsiri W, Bornman MSR, Hayes VM, Elnitski L. MethylToSNP: identifying SNPs in Illumina DNA methylation array data. Epigenetics Chromatin, 12(1), pp. 79. doi:10.1186/s13072-019-0321-6 (20 December 2019)

Ward CM, Thu-Hien T, Pederson SM. ngsReports: A Bioconductor package for managing FastQC reports and other NGS related log files. Bioinformatics. doi:10.1093/bioinformatics/btz937 (16 December 2019)

Waardenberg AJ, Field MA. consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction. PeerJ, 7, pp. e8206. doi:10.7717/peerj.8206 (13 December 2019)

Cheung K, Burgers MJ, Young DA, Cockell S, Reynard LN. Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage. Epigenetics, pp. 1-10. doi:10.1080/15592294.2019.1700003 (13 December 2019)

Labudová D, Hon J, Lexa M. pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. Bioinformatics. doi:10.1093/bioinformatics/btz928 (12 December 2019)

Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC. Publisher Correction: Orchestrating single-cell analysis with Bioconductor. Nat Methods. doi:10.1038/s41592-019-0700-8 (11 December 2019)

Ahmed M, Kim DR. Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes. Adipocyte, 8(1), pp. 401-411. doi:10.1080/21623945.2019.1697563 (7 December 2019)

Qiu CC, Su QS, Zhu SY, Liu RC. Identification of Potential Biomarkers and Biological Pathways in Juvenile Dermatomyositis Based on miRNA-mRNA Network. Biomed Res Int, 2019, pp. 7814287. doi:10.1155/2019/7814287 (7 December 2019)

Chao KH, Hsiao YW, Lee YF, Lee CY, Lai LC, Tsai MH, Lu TP, Chuang EY. RNASeqR: an R package for automated two-group RNA-Seq analysis workflow. IEEE/ACM Trans Comput Biol Bioinform. doi:10.1109/TCBB.2019.2956708 (2 December 2019)

Gustavsen JA, Pai S, Isserlin R, Demchak B, Pico AR. RCy3: Network biology using Cytoscape from within R. F1000Res, 8, pp. 1774. doi:10.12688/f1000research.20887.3 (18 October 2019)

Weber LM, Soneson C. HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats. F1000Res, 8, pp. 1459. doi:10.12688/f1000research.20210.2 (19 August 2019)