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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 2016-05-25T11:00:12-04:00.

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)
Hombach D, Schwarz JM, Robinson PN, Schuelke M, Seelow D. A systematic, large-scale comparison of transcription factor binding site models BMC Genomics, 17, pp. 388. doi:10.1186/s12864-016-2729-8 (21 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)
Voutsina N, Payne AC, Hancock RD, Clarkson GJ, Rothwell SD, Chapman MA, Taylor G. Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health BMC Genomics, 17, pp. 378. doi:10.1186/s12864-016-2704-4 (20 May 2016)
Goralski M, Sobieszczanska P, Obrepalska-Steplowska A, Swiercz A, Zmienko A, Figlerowicz M. A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly Plant Methods, 12, pp. 28. doi:10.1186/s13007-016-0128-4 (20 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)
Patmanathan SN, Johnson SP, Lai SL, Panja Bernam S, Lopes V, Wei W, Ibrahim MH, Torta F, Narayanaswamy P, Wenk MR, Herr DR, Murray PG, Yap LF, Paterson IC. Aberrant expression of the S1P regulating enzymes, SPHK1 and SGPL1, contributes to a migratory phenotype in OSCC mediated through S1PR2 Sci Rep, 6, pp. 25650. doi:10.1038/srep25650 (10 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)
Mieczkowski J, Cook A, Bowman SK, Mueller B, Alver BH, Kundu S, Deaton AM, Urban JA, Larschan E, Park PJ, Kingston RE, Tolstorukov MY. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility Nat Commun, 7, pp. 11485. doi:10.1038/ncomms11485 (6 May 2016)
Martín G, Leivar P, Ludevid D, Tepperman JM, Quail PH, Monte E. Phytochrome and retrograde signalling pathways converge to antagonistically regulate a light-induced transcriptional network Nat Commun, 7, pp. 11431. doi:10.1038/ncomms11431 (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)
Martinez-Martin N, Ramani SR, Hackney JA, Tom I, Wranik BJ, Chan M, Wu J, Paluch MT, Takeda K, Hass PE, Clark H, Gonzalez LC. The extracellular interactome of the human adenovirus family reveals diverse strategies for immunomodulation Nat Commun, 7, pp. 11473. doi:10.1038/ncomms11473 (5 May 2016)


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