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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 2019-06-25T18:20:07-04:00.

Wang X, Gao J, Zhou B, Xie J, Zhou G, Chen Y. Identification of prognostic markers for hepatocellular carcinoma based on miRNA expression profiles. Life Sci, pp. 116596. doi:10.1016/j.lfs.2019.116596 (21 June 2019)
Vertii A, Ou J, Yu J, Yan A, Pagès H, Liu H, Zhu LJ, Kaufman PD. Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin. Genome Res. doi:10.1101/gr.247072.118 (14 June 2019)
Mauguen A, Seshan VE, Begg CB, Ostrovnaya I. Testing Clonal Relatedness of Two Tumors from the Same Patient based on their Mutational Profiles: update of the Clonality R Package. Bioinformatics. doi:10.1093/bioinformatics/btz486 (14 June 2019)
Agius P, Geiger H, Robine N. SCANVIS: a tool for SCoring, ANnotating and VISualizing splice junctions. Bioinformatics. doi:10.1093/bioinformatics/btz452 (14 June 2019)
Marini F, Binder H. pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components. BMC Bioinformatics, 20(1), pp. 331. doi:10.1186/s12859-019-2879-1 (13 June 2019)
Thomas AM, Cabrera CP, Finlay M, Lall K, Nobles M, Schilling RJ, Wood K, Mein CA, Barnes MR, Munroe PB, Tinker A. Differentially Expressed Genes for Atrial Fibrillation Identified using RNA Sequencing from Paired Human Left and Right Atrial Appendages. Physiol Genomics. doi:10.1152/physiolgenomics.00012.2019 (7 June 2019)
Crookenden MA, Moyes KM, Kuhn-Sherlock B, Lehnert K, Walker CG, Loor JJ, Mitchell MD, Murray A, Dukkipati VSR, Vailati-Riboni M, Heiser A, Roche JR. Transcriptomic analysis of circulating neutrophils in metabolically stressed peripartal grazing dairy cows. J Dairy Sci. doi:10.3168/jds.2019-16367 (6 June 2019)
Perkins P, Mazzoni-Putman S, Stepanova A, Alonso J, Heber S. RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data. BMC Genomics, 20(Suppl 5), pp. 422. doi:10.1186/s12864-019-5700-7 (6 June 2019)
Ou J, Zhu LJ. trackViewer: a Bioconductor package for interactive and integrative visualization of multi-omics data. Nat Methods, 16(6), pp. 453-454. doi:10.1038/s41592-019-0430-y (28 May 2019)
El Amrani K, Alanis-Lobato G, Mah N, Kurtz A, Andrade-Navarro MA. Detection of condition-specific marker genes from RNA-seq data with MGFR. PeerJ, 7, pp. e6970. doi:10.7717/peerj.6970 (27 May 2019)
Kolpakov F, Akberdin I, Kashapov T, Kiselev L, Kolmykov S, Kondrakhin Y, Kutumova E, Mandrik N, Pintus S, Ryabova A, Sharipov R, Yevshin I, Kel A. BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. Nucleic Acids Res. doi:10.1093/nar/gkz440 (27 May 2019)
Gonzalo Sanz R, Sánchez-Pla A. Statistical Analysis of Microarray Data. Methods Mol Biol, 1986, pp. 87-121. doi:10.1007/978-1-4939-9442-7_5 (23 May 2019)
Trino S, Zoppoli P, Carella AM, Laurenzana I, Weisz A, Memoli D, Calice G, La Rocca F, Simeon V, Savino L, Del Vecchio L, Musto P, Caivano A, De Luca L. DNA methylation dynamic of bone marrow hematopoietic stem cells after allogeneic transplantation. Stem Cell Res Ther, 10(1), pp. 138. doi:10.1186/s13287-019-1245-6 (20 May 2019)
Delmonico L, Attiya S, Chen JW, Obenauer JC, Goodwin EC, Fournier MV. Expression Concordance of 325 Novel RNA Biomarkers between Data Generated by NanoString nCounter and Affymetrix GeneChip. Dis Markers, 2019, pp. 1940347. doi:10.1155/2019/1940347 (14 May 2019)
Orjuela S, Huang R, Hembach KM, Robinson MD, Soneson C. ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data. G3 (Bethesda). doi:10.1534/g3.119.400185 (14 May 2019)
Wang TT, Lee CY, Lai LC, Tsai MH, Lu TP, Chuang EY. anamiR: integrated analysis of MicroRNA and gene expression profiling. BMC Bioinformatics, 20(1), pp. 239. doi:10.1186/s12859-019-2870-x (14 May 2019)
Goksuluk D, Zararsiz G, Korkmaz S, Eldem V, Zararsiz GE, Ozcetin E, Ozturk A, Karaagaoglu AE. MLSeq: Machine learning interface for RNA-sequencing data. Comput Methods Programs Biomed, 175, pp. 223-231. doi:10.1016/j.cmpb.2019.04.007 (29 April 2019)
Crook OM, Breckels LM, Lilley KS, Kirk PDW, Gatto L. A Bioconductor workflow for the Bayesian analysis of spatial proteomics. F1000Res, 8, pp. 446. doi:10.12688/f1000research.18636.1 (11 April 2019)
Li Z, Zuo Y, Xu C, Varghese RS, Ressom HW. INDEED: R package for network based differential expression analysis. Proceedings (IEEE Int Conf Bioinformatics Biomed), 2018, pp. 2709-2712. doi:10.1109/BIBM.2018.8621426 (24 January 2019)
Mah CK, Mesirov JP, Chavez L. An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays. F1000Res, 7. doi:10.12688/f1000research.16338.1 (5 December 2018)

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