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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 2022-08-10T17:30:11-04:00.

Bürger A, Dugas M. Cogito: automated and generic comparison of annotated genomic intervals. BMC Bioinformatics, 23(1), pp. 315. doi:10.1186/s12859-022-04853-1 (4 August 2022)
Iida K, Kondo J, Wibisana JN, Inoue M, Okada M. ASURAT: Functional annotation-driven unsupervised clustering of single-cell transcriptomes. Bioinformatics. doi:10.1093/bioinformatics/btac541 (4 August 2022)
Bennett AN, Rainford J, Huang X, He Q, Chan KHK. Canary: an automated tool for the conversion of MaCH imputed dosage files to PLINK files. BMC Bioinformatics, 23(1), pp. 304. doi:10.1186/s12859-022-04822-8 (27 July 2022)
Wang L, Yuan L. Analysis of ginseng in the treatment of Interstitial Cystitis/Bladder Pain Syndrome based on network pharmacology. Eur Rev Med Pharmacol Sci, 26(13), pp. 4709-4720. doi:10.26355/eurrev_202207_29196 (21 July 2022)
Gu Z, Hübschmann D. pkgndep: a tool for analyzing dependency heaviness of R packages. Bioinformatics. doi:10.1093/bioinformatics/btac449 (8 July 2022)
Yu J, Luo X. Identification of Cell-Type-Specific Spatially Variable Genes Accounting for Excess Zeros. Bioinformatics. doi:10.1093/bioinformatics/btac457 (6 July 2022)
Qian X, Zhang L, Xie F, Cheng Y, Cui D. Network-Based Pharmacological Study on the Mechanism of Guishao-Liujun Decoction in the Treatment of Gastric Cancer. Front Pharmacol, 13, pp. 937439. doi:10.3389/fphar.2022.937439 (5 July 2022)
Salzer L, Witting M, Schmitt-Kopplin P. MobilityTransformR: An R package for effective mobility transformation of CE-MS data. Bioinformatics. doi:10.1093/bioinformatics/btac441 (4 July 2022)
Cao Y, Dong Q, Wang D, Zhang P, Liu Y, Niu C. microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization. Bioinformatics. doi:10.1093/bioinformatics/btac438 (30 June 2022)
Metwally AA, Zhang T, Wu S, Kellogg R, Zhou W, Contrepois K, Tang H, Snyder M. Robust Identification of Temporal Biomarkers in Longitudinal Omics Studies. Bioinformatics. doi:10.1093/bioinformatics/btac403 (28 June 2022)
Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nat Commun, 13(1), pp. 3695. doi:10.1038/s41467-022-31411-3 (27 June 2022)
Arslan T, Pan Y, Mermelekas G, Vesterlund M, Orre LM, Lehtiö J. SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry. Nat Protoc, 17(8), pp. 1832-1867. doi:10.1038/s41596-022-00699-2 (22 June 2022)
Persson S, Larsson C, Simonsson M, Ellström P. rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses. BMC Bioinformatics, 23(1), pp. 239. doi:10.1186/s12859-022-04781-0 (18 June 2022)
Wang ZB, Qu J, Yang ZY, Liu DY, Jiang SL, Zhang Y, Yang ZQ, Mao XY, Liu ZQ. Integrated Analysis of Expression Profile and Potential Pathogenic Mechanism of Temporal Lobe Epilepsy With Hippocampal Sclerosis. Front Neurosci, 16, pp. 892022. doi:10.3389/fnins.2022.892022 (16 June 2022)
Han Y, Quan X, Chuang Y, Liang Q, Li Y, Yuan Z, Bian Y, Wei L, Wang J, Zhao Y. A multi-omics analysis for the prediction of neurocognitive disorders risk among the elderly in Macao. Clin Transl Med, 12(6), pp. e909. doi:10.1002/ctm2.909 (14 June 2022)
Movassagh M, Morton SU, Hehnly C, Smith J, Doan TT, Irizarry R, Broach JR, Schiff SJ, Bailey JA, Paulson JN. mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis. BMC Genomics, 23(1), pp. 439. doi:10.1186/s12864-022-08558-w (13 June 2022)
Pardo B, Spangler A, Weber LM, Page SC, Hicks SC, Jaffe AE, Martinowich K, Maynard KR, Collado-Torres L. spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data. BMC Genomics, 23(1), pp. 434. doi:10.1186/s12864-022-08601-w (10 June 2022)
Song Y, Feng T, Cao W, Yu H, Zhang Z. Identification of Key Genes in Nasopharyngeal Carcinoma Based on Bioinformatics Analysis. Comput Intell Neurosci, 2022, pp. 9022700. doi:10.1155/2022/9022700 (7 June 2022)
Macedo-da-Silva J, Coutinho JVP, Rosa-Fernandes L, Marie SKN, Palmisano G. Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data. Adv Protein Chem Struct Biol, 131, pp. 311-339. doi:10.1016/bs.apcsb.2022.04.002 (12 May 2022)
Germain PL, Lun A, Garcia Meixide C, Macnair W, Robinson MD. Doublet identification in single-cell sequencing data using scDblFinder. F1000Res, 10, pp. 979. doi:10.12688/f1000research.73600.2 (28 September 2021)

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