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Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.
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). PMC4509590
Kannan L, et al. (2015). Public data and open source tools for multi-assay genomic investigation of disease. Brief Bioinform. doi:10.1093/bib/bbv080
Love M, Huber W, and Anders S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550; doi:10.1186/s13059-014-0550-8
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

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2017-01-16T23:20:10-05:00.

McCarthy DJ, Campbell KR, Lun AT, Wills QF. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics. doi:10.1093/bioinformatics/btw777 (14 January 2017)
Lai YP, Wang LB, Wang WA, Lai LC, Tsai MH, Lu TP, Chuang EY. iGC-an integrated analysis package of gene expression and copy number alteration. BMC Bioinformatics, 18(1), pp. 35. doi:10.1186/s12859-016-1438-2 (14 January 2017)
Novianti PW, Snoek BC, Wilting SM, van de Wiel MA. Better diagnostic signatures from RNAseq data through use of auxiliary co-data. Bioinformatics. doi:10.1093/bioinformatics/btw837 (10 January 2017)
Koper A, Zeef LA, Joseph L, Kerr K, Gosney J, Lindsay MA, Booton R. Whole Transcriptome Analysis of Pre-invasive and Invasive Early Squamous Lung Carcinoma in Archival Laser Microdissected Samples. Respir Res, 18(1), pp. 12. doi:10.1186/s12931-016-0496-3 (10 January 2017)
Sattler C, Moritz F, Chen S, Steer B, Kutschke D, Irmler M, Beckers J, Eickelberg O, Schmitt-Kopplin P, Adler H, Stoeger T. Nanoparticle exposure reactivates latent herpesvirus and restores a signature of acute infection Part Fibre Toxicol, 14, pp. 2. doi:10.1186/s12989-016-0181-1 (10 January 2017)
Chen Q, Li M, Zhang Z, Tie W, Chen X, Jin L, Zhai N, Zheng Q, Zhang J, Wang R, Xu G, Zhang H, Liu P, Zhou H. Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco BMC Genomics, 18, pp. 62. doi:10.1186/s12864-016-3372-0 (10 January 2017)
Guan Y, Liang G, Martin GB, Guan LL. Functional changes in mRNA expression and alternative pre-mRNA splicing associated with the effects of nutrition on apoptosis and spermatogenesis in the adult testis BMC Genomics, 18, pp. 64. doi:10.1186/s12864-016-3385-8 (10 January 2017)
McCann KE, Sinkiewicz DM, Norvelle A, Huhman KL. De novo assembly, annotation, and characterization of the whole brain transcriptome of male and female Syrian hamsters Sci Rep, 7, pp. 40472. doi:10.1038/srep40472 (10 January 2017)
Zamani-Ahmadmahmudi M, Aghasharif S, Ilbeigi K. Prognostic efficacy of the human B-cell lymphoma prognostic genes in predicting disease-free survival (DFS) in the canine counterpart BMC Vet Res, 13, pp. 17. doi:10.1186/s12917-016-0919-x (9 January 2017)
Straube J, Huang BE, Cao KA. DynOmics to identify delays and co-expression patterns across time course experiments Sci Rep, 7, pp. 40131. doi:10.1038/srep40131 (9 January 2017)
Rau A, Maugis-Rabusseau C. Transformation and model choice for RNA-seq co-expression analysis. Brief Bioinform. doi:10.1093/bib/bbw128 (8 January 2017)
Harshbarger J, Kratz A, Carninci P. DEIVA: a web application for interactive visual analysis of differential gene expression profiles BMC Genomics, 18, pp. 47. doi:10.1186/s12864-016-3396-5 (7 January 2017)
Fresno C, González GA, Merino GA, Flesia AG, Podhajcer OL, Llera AS, Fernández EA. A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm. Bioinformatics. doi:10.1093/bioinformatics/btw704 (6 January 2017)
Shannon CP, Balshaw R, Chen V, Hollander Z, Toma M, McManus BM, FitzGerald JM, Sin DD, Ng RT, Tebbutt SJ. Enumerateblood – an R package to estimate the cellular composition of whole blood from Affymetrix Gene ST gene expression profiles BMC Genomics, 18, pp. 43. doi:10.1186/s12864-016-3460-1 (6 January 2017)
Tebel K, Boldt V, Steininger A, Port M, Ebert G, Ullmann R. GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants BMC Bioinformatics, 18, pp. 19. doi:10.1186/s12859-016-1430-x (6 January 2017)
Aquino P, Honda B, Jaini S, Lyubetskaya A, Hosur K, Chiu JG, Ekladious I, Hu D, Jin L, Sayeg MK, Stettner AI, Wang J, Wong BG, Wong WS, Alexander SL, Ba C, Bensussen SI, Bernstein DB, Braff D, Cha S, Cheng DI, Cho JH, Chou K, Chuang J, Gastler DE, Grasso DJ, Greifenberger JS, Guo C, Hawes AK, Israni DV, Jain SR, Kim J, Lei J, Li H, Li D, Li Q, Mancuso CP, Mao N, Masud SF, Meisel CL, Mi J, Nykyforchyn CS, Park M, Peterson HM, Ramirez AK, Reynolds DS, Rim NG, Saffie JC, Su H, Su WR, Su Y, Sun M, Thommes MM, Tu T, Varongchayakul N, Wagner TE, Weinberg BH, Yang R, Yaroslavsky A, Yoon C, Zhao Y, Zollinger AJ, Stringer AM, Foster JW, Wade J, Raman S, Broude N, Wong WW, Galagan JE. Coordinated regulation of acid resistance in Escherichia coli BMC Syst Biol, 11, pp. 1. doi:10.1186/s12918-016-0376-y (6 January 2017)
Gracio F, Burford B, Gazinska P, Mera A, Mohd Noor A, Marra P, Gillett C, Grigoriadis A, Pinder S, Tutt A, de Rinaldis E. Splicing imbalances in basal-like breast cancer underpin perturbation of cell surface and oncogenic pathways and are associated with patients’ survival Sci Rep, 7, pp. 40177. doi:10.1038/srep40177 (6 January 2017)
Latorre-Estivalis JM, Robertson HM, Walden KK, Ruiz J, Gonçalves LO, Guarneri AA, Lorenzo MG. The molecular sensory machinery of a Chagas disease vector: expression changes through imaginal moult and sexually dimorphic features Sci Rep, 7, pp. 40049. doi:10.1038/srep40049 (6 January 2017)
Shankar RD, Bhattacharya S, Jujjavarapu C, Andorf S, Wiser JA, Butte AJ. RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data. Bioinformatics. doi:10.1093/bioinformatics/btw719 (5 January 2017)
Pedersen TL, Nookaew I, Wayne Ussery D, Månsson M. PanViz: interactive visualization of the structure of functionally annotated pangenomes. Bioinformatics. doi:10.1093/bioinformatics/btw761 (5 January 2017)

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