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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 2021-05-09T08:00:07-04:00.

Eagles NJ, Burke EE, Leonard J, Barry BK, Stolz JM, Huuki L, Phan BN, Serrato VL, Gutiérrez-Millán E, Aguilar-Ordoñez I, Jaffe AE, Collado-Torres L. SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. BMC Bioinformatics, 22(1), pp. 224. doi:10.1186/s12859-021-04142-3 (1 May 2021)

Tian J, Bai Y, Liu A, Luo B. Identification of key biomarkers for thyroid cancer by integrative gene expression profiles. Exp Biol Med (Maywood), pp. 15353702211008809. doi:10.1177/15353702211008809 (25 April 2021)

Maden SK, Thompson RF, Hansen KD, Nellore A. Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. NAR Genom Bioinform, 3(2), pp. lqab025. doi:10.1093/nargab/lqab025 (22 April 2021)

Wu JQ, Mao LB, Liu LF, Li YM, Wu J, Yao J, Zhang FH, Liu TY, Yuan L. Identification of key genes and pathways of BMP-9-induced osteogenic differentiation of mesenchymal stem cells by integrated bioinformatics analysis. J Orthop Surg Res, 16(1), pp. 273. doi:10.1186/s13018-021-02390-w (20 April 2021)

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)

Castillo-Secilla D, Gálvez JM, Carrillo-Perez F, Verona-Almeida M, Redondo-Sánchez D, Ortuno FM, Herrera LJ, Rojas I. KnowSeq R-Bioc package: The automatic smart gene expression tool for retrieving relevant biological knowledge. Comput Biol Med, 133, pp. 104387. doi:10.1016/j.compbiomed.2021.104387 (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)

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)

Serizay J, Ahringer J. periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA. F1000Res, 10, pp. 141. doi:10.12688/f1000research.51143.1 (24 February 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)