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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 2020-09-25T01:40:08-04:00.

Peter S, Pendergraft A, VanDerPol W, Wilcox CM, Kyanam Kabir Baig KR, Morrow C, Izard J, Mannon PJ. Mucosa-Associated Microbiota in Barrett's Esophagus, Dysplasia, and Esophageal Adenocarcinoma Differ Similarly Compared With Healthy Controls. Clin Transl Gastroenterol, 11(8), pp. e00199. doi:10.14309/ctg.0000000000000199 (22 September 2020)
Pelegí-Sisó D, de Prado P, Ronkainen J, Bustamante M, González JR. methylclock: a Bioconductor package to estimate DNA methylation age. Bioinformatics. doi:10.1093/bioinformatics/btaa825 (22 September 2020)
Manotas MC, Calderón JC, López-Kleine L, Suárez-Obando F, Moreno OM, Rojas A. Identification of common differentially expressed genes in Turner (45,X) and Klinefelter (47,XXY) syndromes using bioinformatics analysis. Mol Genet Genomic Med, pp. e1503. doi:10.1002/mgg3.1503 (21 September 2020)
Liu P, Soukup AA, Bresnick EH, Dewey CN, Keles S. PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments. Genome Res. doi:10.1101/gr.252445.119 (21 September 2020)
Yu SH, Ferretti D, Schessner JP, Rudolph JD, Borner GHH, Cox J. Expanding the Perseus Software for Omics Data Analysis With Custom Plugins. Curr Protoc Bioinformatics, 71(1), pp. e105. doi:10.1002/cpbi.105 (16 September 2020)
Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. doi:10.1074/mcp.TIR120.002155 (9 September 2020)
Bhagwat AM, Graumann J, Wiegandt R, Bentsen M, Welker J, Kuenne C, Preussner J, Braun T, Looso M. multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets. Life Sci Alliance, 3(11). doi:10.26508/lsa.202000757 (9 September 2020)
Gatto L, Gibb S, Rainer J. MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data. J Proteome Res. doi:10.1021/acs.jproteome.0c00313 (9 September 2020)
Zheng X, Davis JW. SAIGEgds - an efficient statistical tool for large-scale PheWAS with mixed models. Bioinformatics. doi:10.1093/bioinformatics/btaa731 (8 September 2020)
Lawson JT, Smith JP, Bekiranov S, Garrett-Bakelman FE, Sheffield NC. COCOA: coordinate covariation analysis of epigenetic heterogeneity. Genome Biol, 21(1), pp. 240. doi:10.1186/s13059-020-02139-4 (7 September 2020)
Nagy Á, Győrffy B. muTarget: A platform linking gene expression changes and mutation status in solid tumors. Int J Cancer. doi:10.1002/ijc.33283 (1 September 2020)
Liu W, Fan Y, Tian C, Jin Y, Du S, Zeng P, Wang A. Deciphering the Molecular Targets and Mechanisms of HGWD in the Treatment of Rheumatoid Arthritis via Network Pharmacology and Molecular Docking. Evid Based Complement Alternat Med, 2020, pp. 7151634. doi:10.1155/2020/7151634 (26 August 2020)
Bass AJ, Storey JD. The optimal discovery procedure for significance analysis of general gene expression studies. Bioinformatics. doi:10.1093/bioinformatics/btaa707 (20 August 2020)
Wang X, Wang L. Screening and Identification of Potential Peripheral Blood Biomarkers for Alzheimer's Disease Based on Bioinformatics Analysis. Med Sci Monit, 26, pp. e924263. doi:10.12659/MSM.924263 (19 August 2020)
Xu Z, Xie C, Taylor JA, Niu L. ipDMR: Identification of differentially methylated regions with interval p-values. Bioinformatics. doi:10.1093/bioinformatics/btaa732 (17 August 2020)
Nwadiugwu MC. Thyroid Tumor: Investigating MicroRNA-21 Gene Suppression in FTC and FTA. Cancer Inform, 19, pp. 1176935120948474. doi:10.1177/1176935120948474 (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(15), pp. 15492-15503. doi:10.18632/aging.103721 (5 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)
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)

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