Home
Help
Publications

Publications

Bioconductor F1000 Research Channel launched!

Featured

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 2023-03-30T20:00:08-04:00.

Pačínková A, Popovici V. IntOMICS: A Bayesian Framework for Reconstructing Regulatory Networks Using Multi-Omics Data. J Comput Biol, pp. 1-6. doi:10.1089/cmb.2022.0149 (24 March 2023)

Guo B, Hicks SC. escheR: Unified multi-dimensional visualizations with Gestalt principles. bioRxiv. doi:10.1101/2023.03.18.533302 (23 March 2023)

Skog S, Örkenby L, Kugelberg U, Öst A, Nätt D. Seqpac: A framework for sRNA-seq analysis in R using sequence-based counts. Bioinformatics. doi:10.1093/bioinformatics/btad144 (21 March 2023)

Geistlinger L, Vargas R, Lee T, Pan J, Huttlin EL, Gentleman R. BioPlexR and BioPlexPy: integrated data products for the analysis of human protein interactions. Bioinformatics, 39(3). doi:10.1093/bioinformatics/btad091 (1 March 2023)

Chen R, Jiang M, Hu B, Fu B, Sun T. Comprehensive Analysis of the Expression, Prognosis, and Biological Significance of PLOD Family in Bladder Cancer. Int J Gen Med, 16, pp. 707-722. doi:10.2147/IJGM.S399875 (24 February 2023)

Maden SK, Walsh B, Ellrott K, Hansen KD, Thompson RF, Nellore A. recountmethylation enables flexible analysis of public blood DNA methylation array data. Bioinform Adv, 3(1), pp. vbad020. doi:10.1093/bioadv/vbad020 (20 February 2023)

Zhao YX, Ma LB, Yang Z, Wang F, Wang HY, Dang JY. Cancerous inhibitor of protein phosphatase 2A enhances chemoresistance of gastric cancer cells to oxaliplatin. World J Gastrointest Oncol, 15(2), pp. 286-302. doi:10.4251/wjgo.v15.i2.286 (15 February 2023)

Guo Z, Shafik AM, Jin P, Wu Z, Wu H. Analyzing mRNA Epigenetic Sequencing Data with TRESS. Methods Mol Biol, 2624, pp. 163-183. doi:10.1007/978-1-0716-2962-8_12 (2 February 2023)

Klein HU. demuxmix: Demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models. bioRxiv. doi:10.1101/2023.01.27.525961 (29 January 2023)

Beg A, Parveen R, Fouad H, Yahia ME, Hassanein AS. Identification of Driver Genes and miRNAs in Ovarian Cancer through an Integrated In-Silico Approach. Biology (Basel), 12(2). doi:10.3390/biology12020192 (26 January 2023)

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, 22(2), pp. 350-358. doi:10.1021/acs.jproteome.2c00423 (17 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)

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)

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)

Dong R, Cameron D, Bedo J, Papenfuss AT. svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data. GigaByte, 2022, pp. gigabyte70. doi:10.46471/gigabyte.70 (5 October 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)