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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 2020-08-11T15:20:07-04:00.

Dhamodharan P, Arumugam M. Multiple Gene Expression Dataset Analysis Reveals Toll-Like Receptor Signaling Pathway is Strongly Associated With Chronic Obstructive Pulmonary Disease Pathogenesis. COPD, pp. 1-15. doi:10.1080/15412555.2020.1793314 (5 August 2020)

Xiong Y, Lei J, Zhao J, Feng Y, Qiao T, Zhou Y, Jiang T, Han Y. Gene expression-based clinical predictions in lung adenocarcinoma. Aging (Albany NY), 12. doi:10.18632/aging.103721 (5 August 2020)

Ren X, Kuan PF. RNAAgeCalc: A multi-tissue transcriptional age calculator. PLoS One, 15(8), pp. e0237006. doi:10.1371/journal.pone.0237006 (4 August 2020)

Wei Z, Qi X, Chen Y, Xia X, Zheng B, Sun X, Zhang G, Wang L, Zhang Q, Xu C, Jiang S, Li X, Xie B, Liao X, Zhu A. Bioinformatics method combined with logistic regression analysis reveal potentially important miRNAs in ischemic stroke. Biosci Rep. doi:10.1042/BSR20201154 (3 August 2020)

Wang F, Zhao N, Gao G, Deng HB, Wang ZH, Deng LL, Yang Y, Lu C. Prognostic value of TP53 co-mutation status combined with EGFR mutation in patients with lung adenocarcinoma. J Cancer Res Clin Oncol. doi:10.1007/s00432-020-03340-5 (2 August 2020)

Arslan AA, Tuminello S, Yang L, Zhang Y, Durmus N, Snuderl M, Heguy A, Zeleniuch-Jacquotte A, Shao Y, Reibman J. Genome-Wide DNA Methylation Profiles in Community Members Exposed to the World Trade Center Disaster. Int J Environ Res Public Health, 17(15). doi:10.3390/ijerph17155493 (30 July 2020)

Hoffman GE, Roussos P. dream: Powerful differential expression analysis for repeated measures designs. Bioinformatics. doi:10.1093/bioinformatics/btaa687 (30 July 2020)

Utturkar S, Dassanayake A, Nagaraju S, Brown SD. Bacterial Differential Expression Analysis Methods. Methods Mol Biol, 2096, pp. 89-112. doi:10.1007/978-1-0716-0195-2_8 (29 July 2020)

Tremblay K, Brisson D, Gaudet D. Gene expression profiles of recurrent acute pancreatitis risk in patients with sustained chylomicronemia. Endocr J. doi:10.1507/endocrj.EJ20-0123 (29 July 2020)

Kurzawa N, Mateus A, Savitski MM. Rtpca: an R package for differential thermal proximity coaggregation analysis. Bioinformatics. doi:10.1093/bioinformatics/btaa682 (27 July 2020)

Cresswell KG, Stansfield JC, Dozmorov MG. SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering. BMC Bioinformatics, 21(1), pp. 319. doi:10.1186/s12859-020-03652-w (20 July 2020)

de Pretis S, Furlan M, Pelizzola M. INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species. Front Genet, 11, pp. 759. doi:10.3389/fgene.2020.00759 (17 July 2020)

Huang T, Choi M, Tzouros M, Golling S, Pandya NJ, Banfai B, Dunkley T, Vitek O. MSstatsTMT: Statistical detection of differentially abundant proteins in experiments with isobaric labeling and multiple mixtures. Mol Cell Proteomics. doi:10.1074/mcp.RA120.002105 (17 July 2020)

Ventero MP, Espinosa N, Jover R, Guillen Y, Merino E, Rodríguez JC. Evolution of intestinal microbiome in a process of faecal microbiota transfer (FMT) in a patient with Clostridioides difficile infection: NGS analysis with different software programs. Enferm Infecc Microbiol Clin. doi:10.1016/j.eimc.2020.05.023 (14 July 2020)

Huang Z, He Z, Kong Y, Liu Z, Gong L. Insight into osteoarthritis through integrative analysis of metabolomics and transcriptomics. Clin Chim Acta, 510, pp. 323-329. doi:10.1016/j.cca.2020.07.010 (10 July 2020)

Thrash A, Warburton ML. A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information. J Vis Exp(161). doi:10.3791/61268 (1 July 2020)

Tran D, Nguyen H, Le U, Bebis G, Luu HN, Nguyen T. A Novel Method for Cancer Subtyping and Risk Prediction Using Consensus Factor Analysis. Front Oncol, 10, pp. 1052. doi:10.3389/fonc.2020.01052 (24 June 2020)

Maremanda KP, Sundar IK, Li D, Rahman I. Age-dependent assessment of genes involved in cellular senescence, telomere and mitochondrial pathways in human lung tissue of smokers, COPD and IPF: Associations with SARS-CoV-2 COVID-19 ACE2-TMPRSS2-Furin-DPP4 axis. Res Sq. doi:10.21203/rs.3.rs-35347/v1 (15 June 2020)

Wagner J, Kancherla J, Braccia D, Matsumara J, Felix V, Crabtree J, Mahurkar A, Corrada Bravo H. Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz. F1000Res, 9, pp. 601. doi:10.12688/f1000research.24345.1 (12 June 2020)

Soneson C, Marini F, Geier F, Love MI, Stadler MB. ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R. F1000Res, 9, pp. 512. doi:10.12688/f1000research.24187.1 (4 June 2020)