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Ramos, M, et al. (2017) Software for the Integration of Multiomics Experiments in Bioconductor Cancer Research 77:e39-e42. doi:10.1158/0008-5472.CAN-17-0344
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 2019-04-21T23:40:07-04:00.

Sherman TD, Kagohara LT, Cao R, Cheng R, Satriano M, Considine M, Krigsfeld G, Ranaweera R, Tang Y, Jablonski SA, Stein-O'Brien G, Gaykalova DA, Weiner LM, Chung CH, Fertig EJ. CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. PLoS Comput Biol, 14(4), pp. e1006935. doi:10.1371/journal.pcbi.1006935 (19 April 2019)
Krüger S, Piro RM. decompTumor2Sig: identification of mutational signatures active in individual tumors. BMC Bioinformatics, 20(Suppl 4), pp. 152. doi:10.1186/s12859-019-2688-6 (18 April 2019)
Li K, Hu F, Xiong W, Wei Q, Liu FF. Network-based transcriptomic analysis reveals novel melatonin-sensitive genes in cardiovascular system. Endocrine. doi:10.1007/s12020-019-01925-w (15 April 2019)
Vitting-Seerup K, Sandelin A. IsoformSwitchAnalyzeR: Analysis of changes in genome-wide patterns of alternative splicing and its functional consequences. Bioinformatics. doi:10.1093/bioinformatics/btz247 (15 April 2019)
Lefort G, Liaubet L, Canlet C, Tardivel P, Père MC, Quesnel H, Paris A, Iannuccelli N, Vialaneix N, Servien R. ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra. Bioinformatics. doi:10.1093/bioinformatics/btz248 (12 April 2019)
Liu Q, Hu Q, Yao S, Kwan ML, Roh JM, Zhao H, Ambrosone CB, Kushi LH, Liu S, Zhu Q. SeqSQC: A Bioconductor Package for Evaluating the Sample Quality of Next-generation Sequencing Data. Genomics Proteomics Bioinformatics. doi:10.1016/j.gpb.2018.07.006 (5 April 2019)
Jiménez-Jacinto V, Sanchez-Flores A, Vega-Alvarado L. Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis. Front Genet, 10, pp. 279. doi:10.3389/fgene.2019.00279 (29 March 2019)
Zhou Y, Zhu J, Tong T, Wang J, Lin B, Zhang J. A statistical normalization method and differential expression analysis for RNA-seq data between different species. BMC Bioinformatics, 20(1), pp. 163. doi:10.1186/s12859-019-2745-1 (29 March 2019)
Kangeyan D, Dunford A, Iyer S, Stewart C, Hanna M, Getz G, Aryee MJ. A (fire)cloud-based DNA methylation data preprocessing and quality control platform. BMC Bioinformatics, 20(1), pp. 160. doi:10.1186/s12859-019-2750-4 (29 March 2019)
Groeneveld CS, Chagas VS, Jones SJM, Robertson AG, Ponder BAJ, Meyer KB, Castro MAA. RTNsurvival : An R/Bioconductor package for regulatory network survival analysis. Bioinformatics. doi:10.1093/bioinformatics/btz229 (28 March 2019)
Lu Y, Wang X, Dong H, Wang X, Yang P, Han L, Wang Y, Zheng Z, Zhang W, Zhang L. Bioinformatics analysis of microRNA expression between patients with and without latent tuberculosis infections. Exp Ther Med, 17(5), pp. 3977-3988. doi:10.3892/etm.2019.7424 (20 March 2019)
Gorrie-Stone TJ, Smart MC, Saffari A, Malki K, Hannon E, Burrage J, Mill J, Kumari M, Schalkwyk LC. Bigmelon: tools for analysing large DNA methylation datasets. Bioinformatics, 35(6), pp. 981-986. doi:10.1093/bioinformatics/bty713 (15 March 2019)
Robertson DS, Wildenhain J, Javanmard A, Karp NA. onlineFDR: an R package to control the false discovery rate for growing data repositories. Bioinformatics. doi:10.1093/bioinformatics/btz191 (14 March 2019)
Müller F, Scherer M, Assenov Y, Lutsik P, Walter J, Lengauer T, Bock C. RnBeads 2.0: comprehensive analysis of DNA methylation data. Genome Biol, 20(1), pp. 55. doi:10.1186/s13059-019-1664-9 (14 March 2019)
Su W, Sun J, Shimizu K, Kadota K. TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data. BMC Res Notes, 12(1), pp. 133. doi:10.1186/s13104-019-4179-2 (13 March 2019)
Pećina-Šlaus N, Kafka A, Gotovac Jerčić K, Logara M, Bukovac A, Bakarić R, Borovečki F. Comparable Genomic Copy Number Aberrations Differ across Astrocytoma Malignancy Grades. Int J Mol Sci, 20(5). doi:10.3390/ijms20051251 (12 March 2019)
Myint L, Avramopoulos DG, Goff LA, Hansen KD. Linear models enable powerful differential activity analysis in massively parallel reporter assays. BMC Genomics, 20(1), pp. 209. doi:10.1186/s12864-019-5556-x (12 March 2019)
Stamm K, Tomita-Mitchell A, Bozdag S. GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display. BMC Bioinformatics, 20(1), pp. 115. doi:10.1186/s12859-019-2697-5 (6 March 2019)
Schmich F, Kuipers J, Merdes G, Beerenwinkel N. netprioR: a probabilistic model for integrative hit prioritisation of genetic screens. Stat Appl Genet Mol Biol. doi:10.1515/sagmb-2018-0033 (6 March 2019)
Kaleb K, Vesztrocy AW, Altenhoff A, Dessimoz C. Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python. F1000Res, 8, pp. 42. doi:10.12688/f1000research.17548.1 (10 January 2019)

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