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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 2021-12-04T10:00:06-05:00.

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)
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)
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)
Nystrom SL, McKay DJ. Memes: A motif analysis environment in R using tools from the MEME Suite. PLoS Comput Biol, 17(9), pp. e1008991. doi:10.1371/journal.pcbi.1008991 (27 September 2021)
Yue A, Chauve C, Libbrecht MW, Brinkman RR. Automated identification of maximal differential cell populations in flow cytometry data. Cytometry A. doi:10.1002/cyto.a.24503 (24 September 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)
Zheng Y, Cai B, Ren C, Xu H, Du W, Wu Y, Lin F, Zhang H, Quan R. Identification of immune related cells and crucial genes in the peripheral blood of ankylosing spondylitis by integrated bioinformatics analysis. PeerJ, 9, pp. e12125. doi:10.7717/peerj.12125 (7 September 2021)
Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L, Fu X, Liu S, Bo X, Yu G. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (N Y), 2(3), pp. 100141. doi:10.1016/j.xinn.2021.100141 (1 July 2021)

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