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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 2020-02-16T09:00:07-05:00.

Geistlinger L, Csaba G, Santarelli M, Ramos M, Schiffer L, Turaga N, Law C, Davis S, Carey V, Morgan M, Zimmer R, Waldron L. Toward a gold standard for benchmarking gene set enrichment analysis. Brief Bioinform. doi:10.1093/bib/bbz158 (6 February 2020)
Krismer K, Guo Y, Gifford DK. IDR2D identifies reproducible genomic interactions. Nucleic Acids Res. doi:10.1093/nar/gkaa030 (3 February 2020)
Ning YL, Yang ZQ, Xian SX, Lin JZ, Lin XF, Chen WT. Bioinformatics Analysis Identifies Hub Genes and Molecular Pathways Involved in Sepsis-Induced Myopathy. Med Sci Monit, 26, pp. e919665. doi:10.12659/MSM.919665 (2 February 2020)
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)
Cai W, Li H, Zhang Y, Han G. Identification of key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis. PeerJ, 8, pp. e8390. doi:10.7717/peerj.8390 (17 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, 15(2), pp. 479-512. 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)
Hu Y, Wang L, Li Z, Wan Z, Shao M, Wu S, Wang G. Potential Prognostic and Diagnostic Values of CDC6, CDC45, ORC6 and SNHG7 in Colorectal Cancer. Onco Targets Ther, 12, pp. 11609-11621. doi:10.2147/OTT.S231941 (31 December 2019)
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)
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)
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)

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