Bioconductor F1000 Research Channel launched!


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 2016-05-26T11:20:07-04:00.

Goldstein LD, Cao Y, Pau G, Lawrence M, Wu TD, Seshagiri S, Gentleman R. Prediction and Quantification of Splice Events from RNA-Seq Data. PLoS One, 11(5), pp. e0156132. doi:10.1371/journal.pone.0156132 (24 May 2016)
Torres-Oliva M, Almudi I, McGregor AP, Posnien N. A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species BMC Genomics, 17, pp. 392. doi:10.1186/s12864-016-2646-x (24 May 2016)
Clare SE, Gupta A, Choi M, Ranjan M, Lee O, Wang J, Ivancic DZ, Kim JJ, Khan SA. Progesterone receptor blockade in human breast cancer cells decreases cell cycle progression through G2/M by repressing G2/M genes BMC Cancer, 16, pp. 326. doi:10.1186/s12885-016-2355-5 (23 May 2016)
Babonis LS, Martindale MQ, Ryan JF. Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis BMC Evol Biol, 16, pp. 114. doi:10.1186/s12862-016-0683-3 (23 May 2016)
Low LY, Harrison PF, Lin YH, Boyce JD, Rood JI, Cheung JK. RNA-seq analysis of virR and revR mutants of Clostridium perfringens BMC Genomics, 17, pp. 391. doi:10.1186/s12864-016-2706-2 (23 May 2016)
Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. doi:10.1093/bioinformatics/btw313 (20 May 2016)
Wang Z, Murakami R, Yuki K, Yoshida Y, Noda M. Bioinformatic Studies to Predict MicroRNAs with the Potential of Uncoupling RECK Expression from Epithelial–Mesenchymal Transition in Cancer Cells Cancer Inform, 15, pp. 91-102. doi:10.4137/CIN.S34141 (19 May 2016)
Yang SD, Jang SS, Han JA, Park HS, Kim JI. Estimation of Prognostic Marker Genes by Public Microarray Data in Patients with Ovarian Serous Cystadenocarcinoma. Yonsei Med J, 57(4), pp. 872-8. doi:10.3349/ymj.2016.57.4.872 (18 May 2016)
Ji Z, Ji H. TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis. Nucleic Acids Res. doi:10.1093/nar/gkw430 (13 May 2016)
Breckels LM, Holden SB, Wojnar D, Mulvey CM, Christoforou A, Groen A, Trotter MW, Kohlbacher O, Lilley KS, Gatto L. Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics. PLoS Comput Biol, 12(5), pp. e1004920. doi:10.1371/journal.pcbi.1004920 (13 May 2016)
de Marchi R, Sorel M, Mooney B, Fudal I, Goslin K, Kwaśniewska K, Ryan PT, Pfalz M, Kroymann J, Pollmann S, Feechan A, Wellmer F, Rivas S, Graciet E. The N-end rule pathway regulates pathogen responses in plants Sci Rep, 6, pp. 26020. doi:10.1038/srep26020 (13 May 2016)
Andrés-León E, Núñez-Torres R, Rojas AM. miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis Sci Rep, 6, pp. 25749. doi:10.1038/srep25749 (11 May 2016)
Hacquard S, Kracher B, Hiruma K, Münch PC, Garrido-Oter R, Thon MR, Weimann A, Damm U, Dallery JF, Hainaut M, Henrissat B, Lespinet O, Sacristán S, Ver Loren van Themaat E, Kemen E, McHardy AC, Schulze-Lefert P, O'Connell RJ. Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi Nat Commun, 7, pp. 11362. doi:10.1038/ncomms11362 (6 May 2016)
Niu L, Xu Z, Taylor JA. RCP: a novel probe design bias correction method for Illumina Methylation BeadChip. Bioinformatics. doi:10.1093/bioinformatics/btw285 (5 May 2016)
Cotton RJ, Graumann J. readat: An R package for reading and working with SomaLogic ADAT files. BMC Bioinformatics, 17(1), pp. 201. doi:10.1186/s12859-016-1007-8 (4 May 2016)
Popovska-Jankovic K, Noveski P, Jankovic-Velickovic L, Stojnev S, Cukuranovic R, Stefanovic V, Toncheva D, Staneva R, Polenakovic M, Plaseska-Karanfilska D. MicroRNA Profiling in Patients with Upper Tract Urothelial Carcinoma Associated with Balkan Endemic Nephropathy Biomed Res Int, 2016, pp. 7450461. doi:10.1155/2016/7450461 (27 April 2016)
Chabbert CD, Steinmetz LM, Klaus B. DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies. PeerJ, 4, pp. e1981. doi:10.7717/peerj.1981 (26 April 2016)
Bolouri H, Zhao LP, Holland EC. Big data visualization identifies the multidimensional molecular landscape of human gliomas Proc Natl Acad Sci U S A, 113(19), pp. 5394-5399. doi:10.1073/pnas.1601591113 (26 April 2016)
Emera D, Yin J, Reilly SK, Gockley J, Noonan JP. Origin and evolution of developmental enhancers in the mammalian neocortex Proc Natl Acad Sci U S A, 113(19), pp. E2617-E2626. doi:10.1073/pnas.1603718113 (25 April 2016)
Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. A benchmark for RNA-seq quantification pipelines. Genome Biol, 17(1), pp. 74. doi:10.1186/s13059-016-0940-1 (23 April 2016)


Monograph     R Programming for Bioinformatics     Bioconductor Case Studies

Book Chapters

Technical Reports and Working Papers


Literature Search »


Courses & Conferences »

Bioconductor courses and conferences explore R programming and the analysis of genomic data. View catalog of a recent course material.

Packages »

Bioconductor's stable, semi-annual release:

Bioconductor is also available via Docker and Amazon Machine Images.

Fred Hutchinson Cancer Research Center