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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 2018-04-19T21:20:06-04:00.

Perrin L, Loizides-Mangold U, Chanon S, Gobet C, Hulo N, Isenegger L, Weger BD, Migliavacca E, Charpagne A, Betts JA, Walhin JP, Templeman I, Stokes K, Thompson D, Tsintzas K, Robert M, Howald C, Riezman H, Feige JN, Karagounis LG, Johnston JD, Dermitzakis ET, Gachon F, Lefai E, Dibner C. Transcriptomic analyses reveal rhythmic and CLOCK-driven pathways in human skeletal muscle eLife, 7, pp. e34114. doi:10.7554/eLife.34114 (16 April 2018)
Cedoz PL, Prunello M, Brennan K, Gevaert O. MethylMix 2.0: an R package for identifying DNA methylation genes. Bioinformatics. doi:10.1093/bioinformatics/bty156 (14 April 2018)
Bonora E, Bianco F, Stanzani A, Giancola F, Astolfi A, Indio V, Evangelisti C, Martelli AM, Boschetti E, Lugaresi M, Ioannou A, Torresan F, Stanghellini V, Clavenzani P, Seri M, Moonen A, Van Beek K, Wouters M, Boeckxstaens GE, Zaninotto G, Mattioli S, De Giorgio R. INPP4B overexpression and c-KIT downregulation in human achalasia. Neurogastroenterol Motil, pp. e13346. doi:10.1111/nmo.13346 (11 April 2018)
Oghabian A, Greco D, Frilander MJ. IntEREst: intron-exon retention estimator. BMC Bioinformatics, 19(1), pp. 130. doi:10.1186/s12859-018-2122-5 (11 April 2018)
de Oliveira AA, Pastina MM, de Souza VF, da Costa Parrella RA, Noda RW, Simeone ML, Schaffert RE, de Magalhães JV, Damasceno CM, Margarido GR. Genomic prediction applied to high-biomass sorghum for bioenergy production Mol Breed, 38(4), pp. 49. doi:10.1007/s11032-018-0802-5 (10 April 2018)
Wagner J, Chelaru F, Kancherla J, Paulson JN, Zhang A, Felix V, Mahurkar A, Elmqvist N, Corrada Bravo H. Metaviz: interactive statistical and visual analysis of metagenomic data. Nucleic Acids Res, 46(6), pp. 2777-2787. doi:10.1093/nar/gky136 (6 April 2018)
Hong J, Brandt N, Abdul-Rahman F, Yang A, Hughes T, Gresham D. An incoherent feedforward loop facilitates adaptive tuning of gene expression eLife, 7, pp. e32323. doi:10.7554/eLife.32323 (5 April 2018)
Gu Z, Eils R, Schlesner M, Ishaque N. EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations. BMC Genomics, 19(1), pp. 234. doi:10.1186/s12864-018-4625-x (4 April 2018)
Chen WS, Bindra RS, Mo A, Hayman T, Husain Z, Contessa JN, Gaffney SG, Townsend JP, Yu JB. CDKN2A Copy Number Loss Is an Independent Prognostic Factor in HPV-Negative Head and Neck Squamous Cell Carcinoma Front Oncol, 8, pp. 95. doi:10.3389/fonc.2018.00095 (4 April 2018)
Wang GY, Li L, Liu B, Han X, Wang CH, Wang JW. Integrated bioinformatic analysis unveils significant genes and pathways in the pathogenesis of supratentorial primitive neuroectodermal tumor Onco Targets Ther, 11, pp. 1849-1859. doi:10.2147/OTT.S148776 (4 April 2018)
Zheng G, Kanchwala M, Xing C, Yu H. MCM2–7-dependent cohesin loading during S phase promotes sister-chromatid cohesion eLife, 7, pp. e33920. doi:10.7554/eLife.33920 (3 April 2018)
Kiselev VY, Yiu A, Hemberg M. scmap: projection of single-cell RNA-seq data across data sets. Nat Methods. doi:10.1038/nmeth.4644 (2 April 2018)
Yi H, Raman AT, Zhang H, Allen GI, Liu Z. Detecting hidden batch factors through data-adaptive adjustment for biological effects. Bioinformatics, 34(7), pp. 1141-1147. doi:10.1093/bioinformatics/btx635 (1 April 2018)
Mao Z, Wu F, Shan Y. Identification of key genes and miRNAs associated with carotid atherosclerosis based on mRNA-seq data Medicine (Baltimore), 97(13), pp. e9832. doi:10.1097/MD.0000000000009832 (30 March 2018)
Shen H, Wang W, Ni B, Zou Q, Lu H, Wang Z. Exploring the molecular mechanisms of osteosarcoma by the integrated analysis of mRNAs and miRNA microarrays. Int J Mol Med. doi:10.3892/ijmm.2018.3594 (27 March 2018)
Nader JS, Abadie J, Deshayes S, Boissard A, Blandin S, Blanquart C, Boisgerault N, Coqueret O, Guette C, Grégoire M, Pouliquen DL. Characterization of increasing stages of invasiveness identifies stromal/cancer cell crosstalk in rat models of mesothelioma Oncotarget, 9(23), pp. 16311-16329. doi:10.18632/oncotarget.24632 (27 March 2018)
Ke H, Zhao L, Zhang H, Feng X, Xu H, Hao J, Wang S, Yang Q, Zou L, Su X, Wang L, Wu C, Wang Y, Nie J, Jiao B. Loss of TDP43 inhibits progression of triple-negative breast cancer in coordination with SRSF3 Proc Natl Acad Sci U S A, 115(15), pp. E3426-E3435. doi:10.1073/pnas.1714573115 (26 March 2018)
Piulats JM, Kondo J, Endo H, Ono H, Hagihara T, Okuyama H, Nishizawa Y, Tomita Y, Ohue M, Okita K, Oyama H, Bono H, Masuko T, Inoue M. Promotion of malignant phenotype after disruption of the three-dimensional structure of cultured spheroids from colorectal cancer Oncotarget, 9(22), pp. 15968-15983. doi:10.18632/oncotarget.24641 (23 March 2018)
Ding H, Wang W, Califano A. iterClust: a statistical framework for iterative clustering analysis. Bioinformatics. doi:10.1093/bioinformatics/bty176 (22 March 2018)
Jeacock L, Faria J, Horn D. Codon usage bias controls mRNA and protein abundance in trypanosomatids eLife, 7, pp. e32496. doi:10.7554/eLife.32496 (15 March 2018)

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