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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


20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2016-07-29T04:00:13-04:00.

Azad A, Rajwa B, Pothen A. flowVS: channel-specific variance stabilization in flow cytometry. BMC Bioinformatics, 17, pp. 291. doi:10.1186/s12859-016-1083-9 (28 July 2016)
Redmond D, Poran A, Elemento O. Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq Genome Med, 8, pp. 80. doi:10.1186/s13073-016-0335-7 (27 July 2016)
Sarropoulou E, Tsalafouta A, Sundaram AY, Gilfillan GD, Kotoulas G, Papandroulakis N, Pavlidis M. Transcriptomic changes in relation to early-life events in the gilthead sea bream (Sparus aurata) BMC Genomics, 17, pp. 506. doi:10.1186/s12864-016-2874-0 (26 July 2016)
Michna A, Schötz U, Selmansberger M, Zitzelsberger H, Lauber K, Unger K, Hess J. Transcriptomic analyses of the radiation response in head and neck squamous cell carcinoma subclones with different radiation sensitivity: time-course gene expression profiles and gene association networks Radiat Oncol, 11, pp. 94. doi:10.1186/s13014-016-0672-0 (26 July 2016)
Toll A, Salgado R, Espinet B, Díaz-Lagares A, Hernández-Ruiz E, Andrades E, Sandoval J, Esteller M, Pujol RM, Hernández-Muñoz I. MiR-204 silencing in intraepithelial to invasive cutaneous squamous cell carcinoma progression Mol Cancer, 15, pp. 53. doi:10.1186/s12943-016-0537-z (25 July 2016)
Lysenko A, Roznovăţ IA, Saqi M, Mazein A, Rawlings CJ, Auffray C. Representing and querying disease networks using graph databases BioData Min, 9, pp. 23. doi:10.1186/s13040-016-0102-8 (25 July 2016)
Harfuddin Z, Dharmadhikari B, Wong SC, Duan K, Poidinger M, Kwajah S, Schwarz H. Transcriptional and functional characterization of CD137L-dendritic cells identifies a novel dendritic cell phenotype Sci Rep, 6, pp. 29712. doi:10.1038/srep29712 (19 July 2016)
Chen H, Chen W, Liu C, Zhang L, Su J, Zhou X. Relational Network for Knowledge Discovery through Heterogeneous Biomedical and Clinical Features Sci Rep, 6, pp. 29915. doi:10.1038/srep29915 (18 July 2016)
Sato S, Tang YJ, Wei Q, Hirata M, Weng A, Han I, Okawa A, Takeda S, Whetstone H, Nadesan P, Kirsch DG, Wunder JS, Alman BA. Mesenchymal tumors can derive from Ng2/Cspg4 expressing pericytes with β-catenin modulating the neoplastic phenotype Cell Rep, 16(4), pp. 917-927. doi:10.1016/j.celrep.2016.06.058 (14 July 2016)
Song M, He Y, Zhou H, Zhang Y, Li X, Yu Y. Combined analysis of DNA methylome and transcriptome reveal novel candidate genes with susceptibility to bovine Staphylococcus aureus subclinical mastitis Sci Rep, 6, pp. 29390. doi:10.1038/srep29390 (14 July 2016)
Soták M, Czeranková O, Klein D, Jurčacková Z, Li L, Čellárová E. Comparative Transcriptome Reconstruction of Four Hypericum Species Focused on Hypericin Biosynthesis Front Plant Sci, 7, pp. 1039. doi:10.3389/fpls.2016.01039 (13 July 2016)
Arimappamagan A, Kruthika, Dawn R, Paturu K, Santosh V. 332 Molecular Characteristics of Tumor Infiltrating Front in Glioblastoma: Insights Into Molecular Heterogeneity and Implications on Targeted Therapy. Neurosurgery, 63 Suppl 1, pp. 197. doi:10.1227/01.neu.0000489821.05971.a8 (12 July 2016)
Backman TW, Girke T. bioassayR: Cross-Target Analysis of Small Molecule Bioactivity. J Chem Inf Model, 56(7), pp. 1237-42. doi:10.1021/acs.jcim.6b00109 (12 July 2016)
Chandler JD, Wongtrakool C, Banton SA, Li S, Orr ML, Barr DB, Neujahr DC, Sutliff RL, Go Y, Jones DP. Low‐dose oral cadmium increases airway reactivity and lung neuronal gene expression in mice Physiol Rep, 4(13), pp. e12821. doi:10.14814/phy2.12821 (12 July 2016)
Stupnikov A, Tripathi S, de Matos Simoes R, McArt D, Salto-Tellez M, Glazko G, Dehmer M, Emmert-Streib F. samExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files. Bioinformatics. doi:10.1093/bioinformatics/btw475 (10 July 2016)
Waldron L, Riester M, Ramos M, Parmigiani G, Birrer M. The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles. J Natl Cancer Inst, 108(11). doi:10.1093/jnci/djw146 (5 July 2016)
Cormier N, Kolisnik T, Bieda M. Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis. BMC Bioinformatics, 17(1), pp. 270. doi:10.1186/s12859-016-1125-3 (5 July 2016)
Ahamed MT, Danielsson A, Nemes S, Carén H. MethPed: an R package for the identification of pediatric brain tumor subtypes. BMC Bioinformatics, 17(1), pp. 262. doi:10.1186/s12859-016-1144-0 (2 July 2016)
Grote S, Prüfer K, Kelso J, Dannemann M. ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain. Bioinformatics. doi:10.1093/bioinformatics/btw392 (26 June 2016)
Rinaudo P, Boudah S, Junot C, Thévenot EA. biosigner: A New Method for the Discovery of Significant Molecular Signatures from Omics Data. Front Mol Biosci, 3, pp. 26. doi:10.3389/fmolb.2016.00026 (21 June 2016)


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