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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 2021-09-19T07:30:07-04:00.

Scherer M, Gasparoni G, Rahmouni S, Shashkova T, Arnoux M, Louis E, Nostaeva A, Avalos D, Dermitzakis ET, Aulchenko YS, Lengauer T, Lyons PA, Georges M, Walter J. Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR. Epigenetics Chromatin, 14(1), pp. 44. doi:10.1186/s13072-021-00415-6 (16 September 2021)

Skidmore ZL, Campbell KM, Cotto KC, Griffith M, Griffith OL. Exploring the Genomic Landscape of Cancer Patient Cohorts with GenVisR. Curr Protoc, 1(9), pp. e252. doi:10.1002/cpz1.252 (11 September 2021)

Liu F, Liu Y, Du Y, Li Y. MiRNA-130a promotes inflammation to accelerate atherosclerosis via the regulation of proliferator-activated receptor γ (PPARγ) expression. Anatol J Cardiol, 25(9), pp. 630-637. doi:10.5152/AnatolJCardiol.2021.56721 (10 September 2021)

Atta L, Sahoo A, Fan J. VeloViz: RNA velocity informed embeddings for visualizing cellular trajectories. Bioinformatics. doi:10.1093/bioinformatics/btab653 (9 September 2021)

Dankó B, Szikora P, Pór T, Szeifert A, Sebestyén E. SplicingFactory-splicing diversity analysis for transcriptome data. Bioinformatics. doi:10.1093/bioinformatics/btab648 (9 September 2021)

Borella M, Martello G, Risso D, Romualdi C. PsiNorm: a scalable normalization for single-cell RNA-seq data. Bioinformatics. doi:10.1093/bioinformatics/btab641 (9 September 2021)

Ghosh T, Philtron D, Zhang W, Kechris K, Ghosh D. Reproducibility of mass spectrometry based metabolomics data. BMC Bioinformatics, 22(1), pp. 423. doi:10.1186/s12859-021-04336-9 (7 September 2021)

Novoa-Del-Toro EM, Mezura-Montes E, Vignes M, Térézol M, Magdinier F, Tichit L, Baudot A. A multi-objective genetic algorithm to find active modules in multiplex biological networks. PLoS Comput Biol, 17(8), pp. e1009263. doi:10.1371/journal.pcbi.1009263 (30 August 2021)

Hippen AA, Falco MM, Weber LM, Erkan EP, Zhang K, Doherty JA, Vähärautio A, Greene CS, Hicks SC. miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. PLoS Comput Biol, 17(8), pp. e1009290. doi:10.1371/journal.pcbi.1009290 (24 August 2021)

Pal K, Ferrari F. Visualizing and Annotating Hi-C Data. Methods Mol Biol, 2301, pp. 97-132. doi:10.1007/978-1-0716-1390-0_5 (21 August 2021)

Oliveira de Biagi CA Jr, Nociti RP, Brotto DB, Funicheli BO, Cássia Ruy P, Bianchi Ximenez JP, Alves Figueiredo DL, Araújo Silva W Jr. CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis. BMC Genomics, 22(1), pp. 624. doi:10.1186/s12864-021-07918-2 (20 August 2021)

Yan J, Man Z, Gao L, Cai L, Lu Q, Dong J. The role of CpG island methylator phenotype in the clinical course of hepatocellular carcinoma. Bioinformatics. doi:10.1093/bioinformatics/btab600 (18 August 2021)

Li Y, Qin J. A Two-Gene-Based Diagnostic Signature for Ruptured Intracranial Aneurysms. Front Cardiovasc Med, 8, pp. 671655. doi:10.3389/fcvm.2021.671655 (13 August 2021)

Nikolaienko O, Lønning PE, Knappskog S. ramr: an R/Bioconductor package for detection of rare aberrantly methylated regions. Bioinformatics. doi:10.1093/bioinformatics/btab586 (12 August 2021)

Plaza-Florido A, Altmäe S, Esteban FJ, Löf M, Radom-Aizik S, Ortega FB. Cardiorespiratory fitness in children with overweight/obesity: Insights into the molecular mechanisms. Scand J Med Sci Sports. doi:10.1111/sms.14028 (1 August 2021)

Iglesias-Martinez LF, De Kegel B, Kolch W. KBoost: a new method to infer gene regulatory networks from gene expression data. Sci Rep, 11(1), pp. 15461. doi:10.1038/s41598-021-94919-6 (29 July 2021)

Hao M, Zan J. The Identification of Childhood Asthma Progression-Related lncRNAs and mRNAs Suitable as Biomarkers Using Weighted Gene Coexpression Network Analysis. Genet Res (Camb), 2021, pp. 5511507. doi:10.1155/2021/5511507 (27 July 2021)

Zhou T, Yang P, Tang S, Zhu Z, Li X, Yang Z, Wu R, Tian X, Li L. Classification of Lung Adenocarcinoma Based on Immune Checkpoint and Screening of Related Genes. J Oncol, 2021, pp. 5512325. doi:10.1155/2021/5512325 (27 July 2021)

Thompson M, Matsumoto M, Ma T, Senabouth A, Palpant NJ, Powell JE, Nguyen Q. scGPS: Determining Cell States and Global Fate Potential of Subpopulations. Front Genet, 12, pp. 666771. doi:10.3389/fgene.2021.666771 (19 July 2021)

Monteiro de Barros MR, Davies-Morel MCG, Mur LAJ, Creevey CJ, Alison RH, Nash DM. Characterization of an Ex Vivo Equine Endometrial Tissue Culture Model Using Next-Generation RNA-Sequencing Technology. Animals (Basel), 11(7). doi:10.3390/ani11071995 (3 July 2021)