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Alexander TA, Irizarry RA, Bravo HC. Capturing discrete latent structures: choose LDs over PCs. Biostatistics. 2021 Sep 1:kxab030. doi: 10.1093/biostatistics/kxab030. Epub ahead of print. PMID: 34467372.

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. 2022 Jun 27;13(1):3695. doi: 10.1038/s41467-022-31411-3. PMID: 35760813; PMCID: PMC9237024

Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, Culotti A, Ellrott K, Goecks J, Grossman RL, Hall IM, Hansen KD, Lawson J, Leek JT, Luria AO, Mosher S, Morgan M, Nekrutenko A, O'Connor BD, Osborn K, Paten B, Patterson C, Tan FJ, Taylor CO, Vessio J, Waldron L, Wang T, Wuichet K. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genom. 2022 Jan 12;2(1):100085. doi: 10.1016/j.xgen.2021.100085. Epub 2022 Jan 13. PMID: 35199087; PMCID: PMC8863334

He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods. 2022 Mar;19(3):316-322. doi: 10.1038/s41592-022-01408-3. Epub 2022 Mar 11. PMID: 35277707; PMCID: PMC8933848

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2023-01-29T19:30:08-05:00.

Wang XY, Beeraka NM, Xue NN, Yu HM, Yang Y, Liu MX, Nikolenko VN, Liu JQ, Zhao D. Identification of a three-gene prognostic signature for radioresistant esophageal squamous cell carcinoma. World J Clin Oncol, 14(1), pp. 13-26. doi:10.5306/wjco.v14.i1.13 (24 January 2023)

Hsu LL, Culhane AC. Correspondence analysis for dimension reduction, batch integration, and visualization of single-cell RNA-seq data. Sci Rep, 13(1), pp. 1197. doi:10.1038/s41598-022-26434-1 (21 January 2023)

Debrie E, Malfait M, Gabriels R, Declerq A, Sticker A, Martens L, Clement L. Quality Control for the Target Decoy Approach for Peptide Identification. J Proteome Res. doi:10.1021/acs.jproteome.2c00423 (17 January 2023)

Martin EA, Fulcher JM, Zhou M, Monroe ME, Petyuk VA. TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis. J Proteome Res. doi:10.1021/acs.jproteome.2c00570 (11 January 2023)

Kohler D, Kaza M, Pasi C, Huang T, Staniak M, Mohandas D, Sabido E, Choi M, Vitek O. MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments. J Proteome Res. doi:10.1021/acs.jproteome.2c00603 (9 January 2023)

Bastide P, Soneson C, Stern DB, Lespinet O, Gallopin M. A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data. Mol Biol Evol, 40(1). doi:10.1093/molbev/msac269 (4 January 2023)

Almeida-Silva F, Zhao T, Ullrich KK, Schranz ME, Van de Peer Y. syntenet: an R/Bioconductor package for the inference and analysis of synteny networks. Bioinformatics, 39(1). doi:10.1093/bioinformatics/btac806 (1 January 2023)

Calgaro M, Romualdi C, Risso D, Vitulo N. benchdamic: benchmarking of differential abundance methods for microbiome data. Bioinformatics, 39(1). doi:10.1093/bioinformatics/btac778 (1 January 2023)

Vo Ngoc LDT, Osei R, Dohr K, Olsen C, Seneca S, Gheldof A. EDIR: exome database of interspersed repeats. Bioinformatics, 39(1). doi:10.1093/bioinformatics/btac771 (1 January 2023)

Jeanmougin M, Brodal HP, Dietrichson Pharo H, Vedeld HM, Lind GE. PoDCall: positive droplet calling and normalization of droplet digital PCR DNA methylation data. Bioinformatics, 39(1). doi:10.1093/bioinformatics/btac766 (1 January 2023)

Dharmaratne M, Kulkarni AS, Taherian Fard A, Mar JC. scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data. Gigascience, 12. doi:10.1093/gigascience/giac126 (28 December 2022)

Hejazi NS, Boileau P, van der Laan MJ, Hubbard AE. A generalization of moderated statistics to data adaptive semiparametric estimation in high-dimensional biology. Stat Methods Med Res, pp. 9622802221146313. doi:10.1177/09622802221146313 (26 December 2022)

Dozmorov MG, Mu W, Davis ES, Lee S, Triche TJ Jr, Phanstiel DH, Love MI. CTCF: an R/bioconductor data package of human and mouse CTCF binding sites. Bioinform Adv, 2(1), pp. vbac097. doi:10.1093/bioadv/vbac097 (16 December 2022)

Wen Z, Liu F, Lin X, Zhong S, Zhang X, Zhou Z, Jolkkonen J, Liu C, Zhao C. Prognostic Signature for Human Umbilical Cord Mesenchymal Stem Cell Treatment of Ischemic Cerebral Infarction by Integrated Bioinformatic Analysis. Biomed Res Int, 2022, pp. 9973232. doi:10.1155/2022/9973232 (13 December 2022)

Kohler D, Tsai TH, Verschueren E, Huang T, Hinkle T, Phu L, Choi M, Vitek O. MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics. Mol Cell Proteomics, 22(1), pp. 100477. doi:10.1016/j.mcpro.2022.100477 (8 December 2022)

Yuan J, Yan F, Li W, Yuan G. Network pharmacological analysis of Xuefu Zhuyu decoction in the treatment of atherosclerosis. Front Pharmacol, 13, pp. 1069704. doi:10.3389/fphar.2022.1069704 (2 December 2022)

Sorokina O, Sorokin A, Armstrong JD. Synaptome.db: a bioconductor package for synaptic proteomics data. Bioinform Adv, 2(1), pp. vbac086. doi:10.1093/bioadv/vbac086 (12 November 2022)

Zhang J, Liu L, Zhang W, Li X, Zhao C, Li S, Li J, Le TD. miRspongeR 2.0: an enhanced R package for exploring miRNA sponge regulation. Bioinform Adv, 2(1), pp. vbac063. doi:10.1093/bioadv/vbac063 (2 September 2022)

Auer F, Kramer F. RCX-an R package adapting the Cytoscape Exchange format for biological networks. Bioinform Adv, 2(1), pp. vbac020. doi:10.1093/bioadv/vbac020 (31 March 2022)

Badia-I-Mompel P, Vélez Santiago J, Braunger J, Geiss C, Dimitrov D, Müller-Dott S, Taus P, Dugourd A, Holland CH, Ramirez Flores RO, Saez-Rodriguez J. decoupleR: ensemble of computational methods to infer biological activities from omics data. Bioinform Adv, 2(1), pp. vbac016. doi:10.1093/bioadv/vbac016 (8 March 2022)