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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 2021-04-19T03:40:07-04:00.

Guo S, Wu J, Zhou W, Liu X, Liu Y, Zhang J, Jia S, Li J, Wang H. Identification and analysis of key genes associated with acute myocardial infarction by integrated bioinformatics methods. Medicine (Baltimore), 100(15), pp. e25553. doi:10.1097/MD.0000000000025553 (16 April 2021)

Li S, Jiang Z, Chao X, Jiang C, Zhong G. Identification of key immune-related genes and immune infiltration in atrial fibrillation with valvular heart disease based on bioinformatics analysis. J Thorac Dis, 13(3), pp. 1785-1798. doi:10.21037/jtd-21-168 (13 April 2021)

Gerber S, Schratt G, Germain PL. Streamlining differential exon and 3' UTR usage with diffUTR. BMC Bioinformatics, 22(1), pp. 189. doi:10.1186/s12859-021-04114-7 (13 April 2021)

Ge X. iDEP Web Application for RNA-Seq Data Analysis. Methods Mol Biol, 2284, pp. 417-443. doi:10.1007/978-1-0716-1307-8_22 (10 April 2021)

Risso D. Normalization of Single-Cell RNA-Seq Data. Methods Mol Biol, 2284, pp. 303-329. doi:10.1007/978-1-0716-1307-8_17 (10 April 2021)

de Pretis S, Furlan M, Pelizzola M. Identification of Genes Post-Transcriptionally Regulated from RNA-seq: The Case Study of Liver Hepatocellular Carcinoma. Methods Mol Biol, 2284, pp. 271-287. doi:10.1007/978-1-0716-1307-8_15 (10 April 2021)

Zhang J, Liu L, Xu T, Zhang W, Zhao C, Li S, Li J, Rao N, Le TD. miRSM: an R package to infer and analyse miRNA sponge modules in heterogeneous data. RNA Biol, pp. 1-13. doi:10.1080/15476286.2021.1905341 (6 April 2021)

Dinalankara W, Ke Q, Geman D, Marchionni L. An R package for divergence analysis of omics data. PLoS One, 16(4), pp. e0249002. doi:10.1371/journal.pone.0249002 (5 April 2021)

Schefzik R, Flesch J, Goncalves A. Fast identification of differential distributions in single-cell RNA-sequencing data with waddR. Bioinformatics. doi:10.1093/bioinformatics/btab226 (1 April 2021)

Zhao Y, Federico A, Faits T, Manimaran S, Segrè D, Monti S, Johnson WE. animalcules: interactive microbiome analytics and visualization in R. Microbiome, 9(1), pp. 76. doi:10.1186/s40168-021-01013-0 (28 March 2021)

Hu Q, Hutson A, Liu S, Morgan M, Liu Q. Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines. Bioinformatics. doi:10.1093/bioinformatics/btab208 (27 March 2021)

Türei D, Valdeolivas A, Gul L, Palacio-Escat N, Klein M, Ivanova O, Ölbei M, Gábor A, Theis F, Módos D, Korcsmáros T, Saez-Rodriguez J. Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. Mol Syst Biol, 17(3), pp. e9923. doi:10.15252/msb.20209923 (23 March 2021)

Dai Y, Xu A, Li J, Wu L, Yu S, Chen J, Zhao W, Sun XJ, Huang J. CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data. BMC Bioinformatics, 22(1), pp. 138. doi:10.1186/s12859-021-04054-2 (22 March 2021)

Ari Yuka S, Yilmaz A. Network based multifactorial modelling of miRNA-target interactions. PeerJ, 9, pp. e11121. doi:10.7717/peerj.11121 (19 March 2021)

Zhang H, Xie Y, Hu Z, Yu H, Xie X, Ye Y, Xu W, Nian S, Yuan Q. Integrative Analysis of the Expression of SIGLEC Family Members in Lung Adenocarcinoma via Data Mining. Front Oncol, 11, pp. 608113. doi:10.3389/fonc.2021.608113 (16 March 2021)

Kim HAJ, Zeng PYF, Shaikh MH, Mundi N, Ghasemi F, Di Gravio E, Khan H, MacNeil D, Khan MI, Patel K, Mendez A, Yoo J, Fung K, Lang P, Palma DA, Mymryk JS, Barrett JW, Boutros PC, Nichols AC. All HPV-negative head and neck cancers are not the same: Analysis of the TCGA dataset reveals that anatomical sites have distinct mutation, transcriptome, hypoxia, and tumor microenvironment profiles. Oral Oncol, 116, pp. 105260. doi:10.1016/j.oraloncology.2021.105260 (13 March 2021)

Munz M, Khodaygani M, Aherrahrou Z, Busch H, Wohlers I. In silico candidate variant and gene identification using inbred mouse strains. PeerJ, 9, pp. e11017. doi:10.7717/peerj.11017 (11 March 2021)

Planell N, Lagani V, Sebastian-Leon P, van der Kloet F, Ewing E, Karathanasis N, Urdangarin A, Arozarena I, Jagodic M, Tsamardinos I, Tarazona S, Conesa A, Tegner J, Gomez-Cabrero D. STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline. Front Genet, 12, pp. 620453. doi:10.3389/fgene.2021.620453 (4 March 2021)

Whalley C, Payne K, Domingo E, Blake A, Richman S, Brooks J, Batis N, Spruce R, Mehanna H, Nankivell P, Beggs AD. Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA. Epigenomes, 5, pp. 6. doi:10.3390/epigenomes5010006 (19 February 2021)

Nieuwenhuis TO, Halushka MK. HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas. F1000Res, 9, pp. 1210. doi:10.12688/f1000research.26771.2 (8 October 2020)