Home
Help
Publications

Publications

Bioconductor F1000 Research Channel launched!

Featured

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 2021-12-07T10:30:07-05:00.

Cardoso MA, Rizzardi LEA, Kume LW, Groeneveld C, Trefflich S, Morais DAA, Dalmolin RJS, Ponder BAJ, Meyer KB, Castro MAA. TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves. Bioinformatics. doi:10.1093/bioinformatics/btab819 (2 December 2021)

van de Geer WS, van Riet J, van de Werken HJG. ProteoDisco: A flexible R approach to generate customized protein databases for extended search space of novel and variant proteins in proteogenomic studies. Bioinformatics. doi:10.1093/bioinformatics/btab809 (2 December 2021)

Gu Z, Hübschmann D. Make Interactive Complex Heatmaps in R. Bioinformatics. doi:10.1093/bioinformatics/btab806 (2 December 2021)

Ye Y, Barapatre S, Davis MK, Elliston KO, Davatzikos C, Fedorov A, Fillion-Robin JC, Foster I, Gilbertson JR, Lasso A, Miller JV, Morgan M, Pieper S, Raumann BE, Sarachan BD, Savova G, Silverstein JC, Taylor DP, Zelnis JB, Zhang GQ, Cuticchia J, Becich MJ. Open-source Software Sustainability Models: Initial White Paper From the Informatics Technology for Cancer Research Sustainability and Industry Partnership Working Group. J Med Internet Res, 23(12), pp. e20028. doi:10.2196/20028 (2 December 2021)

Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung TY, Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, Vandepoele K, Wasserman WW, Parcy F, Mathelier A. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res. doi:10.1093/nar/gkab1113 (30 November 2021)

Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B. recount3: summaries and queries for large-scale RNA-seq expression and splicing. Genome Biol, 22(1), pp. 323. doi:10.1186/s13059-021-02533-6 (29 November 2021)

Siavoshi A, Taghizadeh M, Dookhe E, Piran M. Gene expression profiles and pathway enrichment analysis to identification of differentially expressed gene and signaling pathways in epithelial ovarian cancer based on high-throughput RNA-seq data. Genomics. doi:10.1016/j.ygeno.2021.11.031 (25 November 2021)

Dong X, Vegesna K, Brouwer C, Luo W. SBGNview: towards data analysis, integration and visualization on all pathways. Bioinformatics. doi:10.1093/bioinformatics/btab793 (23 November 2021)

Almeida-Silva F, Venancio TM. BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction. Funct Integr Genomics. doi:10.1007/s10142-021-00821-9 (17 November 2021)

Naake T, Huber W. MatrixQCvis: shiny-based interactive data quality exploration for omics data. Bioinformatics. doi:10.1093/bioinformatics/btab748 (12 November 2021)

Stilianoudakis SC, Marshall MA, Dozmorov MG. preciseTAD: A transfer learning framework for 3D domain boundary prediction at base-pair resolution. Bioinformatics. doi:10.1093/bioinformatics/btab743 (6 November 2021)

Liu M, Fan G, Zhang D, Zhu M, Zhang H. Study on Mechanism of Jiawei Chaiqin Wendan Decoction in Treatment of Vestibular Migraine Based on Network Pharmacology and Molecular Docking Technology. Evid Based Complement Alternat Med, 2021, pp. 5528403. doi:10.1155/2021/5528403 (31 October 2021)

Ye J, Li L, Hu Z. Exploring the Molecular Mechanism of Action of Yinchen Wuling Powder for the Treatment of Hyperlipidemia, Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation. Biomed Res Int, 2021, pp. 9965906. doi:10.1155/2021/9965906 (28 October 2021)

Mohammadi M, Salehzadeh A, Talesh Sasani S, Tarang A. The miR526b-5p-Related Single Nucleotide Polymorphisms, rs72618599, Located in 3'-UTR of TCF3 Gene, is Associated with the Risk of Breast and Gastric Cancers. Iran Biomed J. doi: (27 October 2021)

Su S, Gouil Q, Blewitt ME, Cook D, Hickey PF, Ritchie ME. NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data. PLoS Comput Biol, 17(10), pp. e1009524. doi:10.1371/journal.pcbi.1009524 (25 October 2021)

Vanderaa C, Gatto L. Replication of single-cell proteomics data reveals important computational challenges. Expert Rev Proteomics, pp. 1-9. doi:10.1080/14789450.2021.1988571 (25 October 2021)

Wright ES. FindNonCoding: rapid and simple detection of non-coding RNAs in genomes. Bioinformatics. doi:10.1093/bioinformatics/btab708 (12 October 2021)

Castellano-Escuder P, Andrés-Lacueva C, Sánchez-Pla A. The fobitools framework: the first steps towards food enrichment analysis. Bioinformatics. doi:10.1093/bioinformatics/btab626 (2 October 2021)

Murphy AE, Schilder BM, Skene NG. MungeSumstats: A Bioconductor package for the standardisation and quality control of many GWAS summary statistics. Bioinformatics. doi:10.1093/bioinformatics/btab665 (2 October 2021)

Huang S, Pang L, Wei C. Identification of a Four-Gene Signature With Prognostic Significance in Endometrial Cancer Using Weighted-Gene Correlation Network Analysis. Front Genet, 12, pp. 678780. doi:10.3389/fgene.2021.678780 (20 September 2021)