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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 2020-10-25T08:40:08-04:00.

Tian R, Zhao G, Zhou A, Li H, Cao B, Guo S. Prognostic gene profiles in the tumor microenvironment of ovarian serous adenocarcinoma. Front Biosci (Landmark Ed), 26, pp. 692-705. doi: (1 January 2021)

Groth EE, Weber M, Bahmer T, Pedersen F, Kirsten A, Börnigen D, Rabe KF, Watz H, Ammerpohl O, Goldmann T. Exploration of the sputum methylome and omics deconvolution by quadratic programming in molecular profiling of asthma and COPD: the road to sputum omics 2.0. Respir Res, 21(1), pp. 274. doi:10.1186/s12931-020-01544-4 (19 October 2020)

Duan Y, Evans DS, Miller RA, Schork NJ, Cummings SR, Girke T. signatureSearch: environment for gene expression signature searching and functional interpretation. Nucleic Acids Res. doi:10.1093/nar/gkaa878 (17 October 2020)

Sherman TD, Gao T, Fertig EJ. CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures. BMC Bioinformatics, 21(1), pp. 453. doi:10.1186/s12859-020-03796-9 (14 October 2020)

Karaduta O, Glazko G, Dvanajscak Z, Arthur J, Mackintosh S, Orr L, Rahmatallah Y, Yeruva L, Tackett A, Zybailov B. Resistant starch slows the progression of CKD in the 5/6 nephrectomy mouse model. Physiol Rep, 8(19), pp. e14610. doi:10.14814/phy2.14610 (11 October 2020)

Bastian FB, Roux J, Niknejad A, Comte A, Fonseca Costa SS, de Farias TM, Moretti S, Parmentier G, de Laval VR, Rosikiewicz M, Wollbrett J, Echchiki A, Escoriza A, Gharib WH, Gonzales-Porta M, Jarosz Y, Laurenczy B, Moret P, Person E, Roelli P, Sanjeev K, Seppey M, Robinson-Rechavi M. The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. Nucleic Acids Res. doi:10.1093/nar/gkaa793 (10 October 2020)

Ahmed M, Min DS, Kim DR. Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations. Adipocyte, 9(1), pp. 600-608. doi:10.1080/21623945.2020.1829852 (6 October 2020)

Shahryary Y, Symeonidi A, Hazarika RR, Denkena J, Mubeen T, Hofmeister B, van Gurp T, Colomé-Tatché M, Verhoeven KJF, Tuskan G, Schmitz RJ, Johannes F. AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. Genome Biol, 21(1), pp. 260. doi:10.1186/s13059-020-02161-6 (6 October 2020)

Zhao Q, Sun Y, Liu Z, Zhang H, Li X, Zhu K, Liu ZX, Ren J, Zuo Z. CrossICC: iterative consensus clustering of cross-platform gene expression data without adjusting batch effect. Brief Bioinform, 21(5), pp. 1818-1824. doi:10.1093/bib/bbz116 (25 September 2020)

Furlan M, Galeota E, Gaudio ND, Dassi E, Caselle M, de Pretis S, Pelizzola M. Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling. Genome Res, 30(10), pp. 1492-1507. doi:10.1101/gr.260984.120 (25 September 2020)

Zhang X, Su Y, Wu X, Xiao R, Wu Y, Yang B, Wang Z, Guo L, Kang X, Wang C. Integrative analysis of the common genetic characteristics in ovarian cancer stem cells sorted by multiple approaches. J Ovarian Res, 13(1), pp. 116. doi:10.1186/s13048-020-00715-7 (25 September 2020)

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, Keleş 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)

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)

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.24187.2 (4 June 2020)