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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 2020-07-03T20:20:07-04:00.

Kaspi A, Ziemann M. mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data. BMC Genomics, 21(1), pp. 447. doi:10.1186/s12864-020-06856-9 (29 June 2020)
Cai J, Drewry MD, Perkumas K, Dismuke WM, Hauser MA, Stamer WD, Liu Y. Differential DNA methylation patterns in human Schlemm's canal endothelial cells with glaucoma. Mol Vis, 26, pp. 483-493. doi: (26 June 2020)
Chávez J, Barberena-Jonas C, Sotelo-Fonseca JE, Alquicira-Hernández J, Salgado H, Collado-Torres L, Reyes A. Programmatic access to bacterial regulatory networks with regutools. Bioinformatics. doi:10.1093/bioinformatics/btaa575 (23 June 2020)
Rutter L, Cook D. bigPint: A Bioconductor visualization package that makes big data pint-sized. PLoS Comput Biol, 16(6), pp. e1007912. doi:10.1371/journal.pcbi.1007912 (15 June 2020)
Gjerga E, Trairatphisan P, Gabor A, Koch H, Chevalier C, Ceccarelli F, Dugourd A, Mitsos A, Saez-Rodriguez J. Converting networks to predictive logic models from perturbation signalling data with CellNOpt. Bioinformatics. doi:10.1093/bioinformatics/btaa561 (9 June 2020)
Forero DA. Available Software for Meta-analyses of Genome-wide Expression Studies. Curr Genomics, 20(5), pp. 325-331. doi:10.2174/1389202920666190822113912 (2 June 2020)
Carey VJ, Ramos M, Stubbs BJ, Gopaulakrishnan S, Oh S, Turaga N, Waldron L, Morgan M. Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale. JCO Clin Cancer Inform, 4, pp. 472-479. doi:10.1200/CCI.19.00111 (27 May 2020)
Wu JX, Pascovici D, Wu Y, Walker AK, Mirzaei M. Workflow for Rapidly Extracting Biological Insights from Complex, Multicondition Proteomics Experiments with WGCNA and PloGO2. J Proteome Res, 19(7), pp. 2898-2906. doi:10.1021/acs.jproteome.0c00198 (22 May 2020)
Odom GJ, Ban Y, Colaprico A, Liu L, Silva TC, Sun X, Pico AR, Zhang B, Wang L, Chen X. PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data. Proteomics, pp. e1900409. doi:10.1002/pmic.201900409 (20 May 2020)
El-Kurdi A, Khalil GA, Khazen G, Khoueiry P. fcScan: a versatile tool to cluster combinations of sites using genomic coordinates. BMC Bioinformatics, 21(1), pp. 194. doi:10.1186/s12859-020-3536-4 (19 May 2020)
Zhao Y, Li K, Sun J, He N, Zhao P, Zang C, Yang X, Hu C, Long J, Zhang H, Wang Q, Zhao Y, Zhang Y. Genomic DNA methylation profiling indicates immune response following thermal ablation treatment for HBV-associated hepatocellular carcinoma. Oncol Lett, 20(1), pp. 677-684. doi:10.3892/ol.2020.11636 (18 May 2020)
Youngblood H, Cai J, Drewry MD, Helwa I, Hu E, Liu S, Yu H, Mu H, Hu Y, Perkumas K, Aboobakar IF, Johnson WM, Stamer WD, Liu Y. Expression of mRNAs, miRNAs, and lncRNAs in Human Trabecular Meshwork Cells Upon Mechanical Stretch. Invest Ophthalmol Vis Sci, 61(5), pp. 2. doi:10.1167/iovs.61.5.2 (11 May 2020)
Chen S, Gao C, Wu Y, Huang Z. Identification of Prognostic miRNA Signature and Lymph Node Metastasis-Related Key Genes in Cervical Cancer. Front Pharmacol, 11, pp. 544. doi:10.3389/fphar.2020.00544 (8 May 2020)
Ishak M, Baharudin R, Rose IM, Sagap I, Mazlan L, Azman ZAM, Abu N, Jamal R, Lee LH, Mutalib NSA. Genome-Wide Open Chromatin Methylome Profiles in Colorectal Cancer. Biomolecules, 10(5). doi:10.3390/biom10050719 (5 May 2020)
Schlosser P, Knaus J, Schmutz M, Dohner K, Plass C, Bullinger L, Claus R, Binder H, Lubbert M, Schumacher M. Netboost: Boosting-supported Network Analysis Improves High-Dimensional Omics Prediction in Acute Myeloid Leukemia and Huntington's Disease. IEEE/ACM Trans Comput Biol Bioinform. doi:10.1109/TCBB.2020.2983010 (1 May 2020)
Andresen AMS, Boudinot P, Gjøen T. Kinetics of transcriptional response against poly (I:C) and infectious salmon anemia virus (ISAV) in Atlantic salmon kidney (ASK) cell line. Dev Comp Immunol, 110, pp. 103716. doi:10.1016/j.dci.2020.103716 (29 April 2020)
Jia L, Liu N, Huang F, Zhou Z, He X, Li H, Wang Z, Yao W. intansv: an R package for integrative analysis of structural variations. PeerJ, 8, pp. e8867. doi:10.7717/peerj.8867 (28 April 2020)
Lee S, Lawrence M, Love MI. Fluent genomics with  plyranges and  tximeta. F1000Res, 9, pp. 109. doi:10.12688/f1000research.22259.1 (12 February 2020)
Ciciani M, Cantore T, Lauria M. rScudo: an R package for classification of molecular profiles using rank-based signatures. Bioinformatics. doi:10.1093/bioinformatics/btaa296 (12 May 2019)

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