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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 2017-02-23T10:00:14-05:00.

Laing EE, Möller-Levet CS, Poh N, Santhi N, Archer SN, Dijk DJ. Blood transcriptome based biomarkers for human circadian phase eLife, 6, pp. e20214. doi:10.7554/eLife.20214 (20 February 2017)
Ma C, Xu S, Liu G, Liu X, Xu X, Wen B, Liu S. Improvement of peptide identification with considering the abundance of mRNA and peptide BMC Bioinformatics, 18, pp. 109. doi:10.1186/s12859-017-1491-5 (16 February 2017)
Ma KS, Li F, Liu Y, Liang PZ, Chen XW, Gao XW. Identification of microRNAs and their response to the stress of plant allelochemicals in Aphis gossypii (Hemiptera: Aphididae) BMC Mol Biol, 18, pp. 5. doi:10.1186/s12867-017-0080-5 (16 February 2017)
Chen Z, Ji L, Wang J, Jin J, Yang X, Rao P, Gao K, Liao W, Ye M, An X. Dynamic changes in the transcriptome of Populus hopeiensis in response to abscisic acid Sci Rep, 7, pp. 42708. doi:10.1038/srep42708 (15 February 2017)
Kumar G, Gupta K, Pathania S, Swarnkar MK, Rattan UK, Singh G, Sharma RK, Singh AK. Chilling Affects Phytohormone and Post-Embryonic Development Pathways during Bud Break and Fruit Set in Apple (Malus domestica Borkh.) Sci Rep, 7, pp. 42593. doi:10.1038/srep42593 (15 February 2017)
Gong H, Liu M, Klomp J, Merrill BJ, Rehman J, Malik AB. Method for Dual Viral Vector Mediated CRISPR-Cas9 Gene Disruption in Primary Human Endothelial Cells Sci Rep, 7, pp. 42127. doi:10.1038/srep42127 (15 February 2017)
Bousios A, Gaut BS, Darzentas N. Considerations and complications of mapping small RNA high-throughput data to transposable elements Mob DNA, 8, pp. 3. doi:10.1186/s13100-017-0086-z (15 February 2017)
Johnson SA, Spollen WG, Manshack LK, Bivens NJ, Givan SA, Rosenfeld CS. Hypothalamic transcriptomic alterations in male and female California mice (Peromyscus californicus) developmentally exposed to bisphenol A or ethinyl estradiol Physiol Rep, 5(3), pp. e13133. doi:10.14814/phy2.13133 (14 February 2017)
Arimilli S, Madahian B, Chen P, Marano K, Prasad GL. Gene expression profiles associated with cigarette smoking and moist snuff consumption BMC Genomics, 18, pp. 156. doi:10.1186/s12864-017-3565-1 (14 February 2017)
Midgett M, López CS, David L, Maloyan A, Rugonyi S. Increased Hemodynamic Load in Early Embryonic Stages Alters Endocardial to Mesenchymal Transition Front Physiol, 8, pp. 56. doi:10.3389/fphys.2017.00056 (8 February 2017)
Parks DR, El Khettabi F, Chase E, Hoffman RA, Perfetto SP, Spidlen J, Wood JC, Moore WA, Brinkman RR. Evaluating flow cytometer performance with weighted quadratic least squares analysis of LED and multi-level bead data. Cytometry A. doi:10.1002/cyto.a.23052 (3 February 2017)
Quiroz-Zárate A, Harshfield BJ, Hu R, Knoblauch N, Beck AH, Hankinson SE, Carey V, Tamimi RM, Hunter DJ, Quackenbush J, Hazra A. Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue. PLoS One, 12(2), pp. e0170181. doi:10.1371/journal.pone.0170181 (2 February 2017)
Zhang Y, Xie J, Yang J, Fennell A, Zhang C, Ma Q. QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data. Bioinformatics, 33(3), pp. 450-452. doi:10.1093/bioinformatics/btw635 (1 February 2017)
Ren X, Yang X, Cheng B, Chen X, Zhang T, He Q, Li B, Li Y, Tang X, Wen X, Zhong Q, Kang T, Zeng M, Liu N, Ma J. HOPX hypermethylation promotes metastasis via activating SNAIL transcription in nasopharyngeal carcinoma Nat Commun, 8, pp. 14053. doi:10.1038/ncomms14053 (1 February 2017)
Cava C, Colaprico A, Bertoli G, Graudenzi A, Silva TC, Olsen C, Noushmehr H, Bontempi G, Mauri G, Castiglioni I. SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data. Int J Mol Sci, 18(2). doi:10.3390/ijms18020274 (27 January 2017)
Wong T, Deveson IW, Hardwick SA, Mercer TR. ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing. Bioinformatics. doi:10.1093/bioinformatics/btx038 (27 January 2017)
Jin J, Li R, Jiang C, Zhang R, Ge X, Liang F, Sheng X, Dai W, Chen M, Wu J, Xiao J, Su W. Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells BMC Genomics, 18(Suppl 1), pp. 933. doi:10.1186/s12864-016-3253-6 (25 January 2017)
Rahmatallah Y, Zybailov B, Emmert-Streib F, Glazko G. GSAR: Bioconductor package for Gene Set analysis in R. BMC Bioinformatics, 18(1), pp. 61. doi:10.1186/s12859-017-1482-6 (24 January 2017)
Wijetunga NA, Johnston AD, Maekawa R, Delahaye F, Ulahannan N, Kim K, Greally JM. SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. BMC Bioinformatics, 18(1), pp. 41. doi:10.1186/s12859-017-1477-3 (18 January 2017)
Hernandez-Ferrer C, Ruiz-Arenas C, Beltran-Gomila A, González JR. MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration. BMC Bioinformatics, 18(1), pp. 36. doi:10.1186/s12859-016-1455-1 (17 January 2017)

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