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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 2017-05-26T10:00:14-04:00.

Suomi T, Seyednasrollah F, Jaakkola MK, Faux T, Elo LL. ROTS: An R package for reproducibility-optimized statistical testing. PLoS Comput Biol, 13(5), pp. e1005562. doi:10.1371/journal.pcbi.1005562 (25 May 2017)
Väremo L, Henriksen TI, Scheele C, Broholm C, Pedersen M, Uhlén M, Pedersen BK, Nielsen J. Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes Genome Med, 9, pp. 47. doi:10.1186/s13073-017-0432-2 (25 May 2017)
Städler N, Dondelinger F, Hill SM, Akbani R, Lu Y, Mills GB, Mukherjee S. Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study. Bioinformatics. doi:10.1093/bioinformatics/btx322 (23 May 2017)
Wang Z, Jin S, Liu G, Zhang X, Wang N, Wu D, Hu Y, Zhang C, Jiang Q, Xu L, Wang Y. DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data BMC Bioinformatics, 18, pp. 270. doi:10.1186/s12859-017-1647-3 (23 May 2017)
Qian Y, Wang C, Wang J, Zhang X, Zhou Z, Zhao M, Lu C. Fipronil-induced enantioselective developmental toxicity to zebrafish embryo-larvae involves changes in DNA methylation Sci Rep, 7, pp. 2284. doi:10.1038/s41598-017-02255-5 (23 May 2017)
Corley SM, MacKenzie KL, Beverdam A, Roddam LF, Wilkins MR. Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols BMC Genomics, 18, pp. 399. doi:10.1186/s12864-017-3797-0 (23 May 2017)
Cimino PJ, Zager M, McFerrin L, Wirsching HG, Bolouri H, Hentschel B, von Deimling A, Jones D, Reifenberger G, Weller M, Holland EC. Multidimensional scaling of diffuse gliomas: application to the 2016 World Health Organization classification system with prognostically relevant molecular subtype discovery Acta Neuropathol Commun, 5, pp. 39. doi:10.1186/s40478-017-0443-7 (22 May 2017)
Lågstad S, Zhao S, Hoff AM, Johannessen B, Christian Lingjærde O, Skotheim RI. chimeraviz: A tool for visualizing chimeric RNA. Bioinformatics. doi:10.1093/bioinformatics/btx329 (19 May 2017)
Zhu LJ, Lawrence M, Gupta A, Pagès H, Kucukural A, Garber M, Wolfe SA. GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases. BMC Genomics, 18(1), pp. 379. doi:10.1186/s12864-017-3746-y (15 May 2017)
Lun ATL, Richard AC, Marioni JC. Testing for differential abundance in mass cytometry data. Nat Methods. doi:10.1038/nmeth.4295 (15 May 2017)
Khomtchouk BB, Hennessy JR, Wahlestedt C. shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics PLoS One, 12(5), pp. e0176334. doi:10.1371/journal.pone.0176334 (11 May 2017)
Contrepois K, Coudereau C, Benayoun BA, Schuler N, Roux PF, Bischof O, Courbeyrette R, Carvalho C, Thuret JY, Ma Z, Derbois C, Nevers MC, Volland H, Redon CE, Bonner WM, Deleuze JF, Wiel C, Bernard D, Snyder MP, Rübe CE, Olaso R, Fenaille F, Mann C. Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression Nat Commun, 8, pp. 14995. doi:10.1038/ncomms14995 (10 May 2017)
Sinha R, Winer AG, Chevinsky M, Jakubowski C, Chen YB, Dong Y, Tickoo SK, Reuter VE, Russo P, Coleman JA, Sander C, Hsieh JJ, Hakimi AA. Analysis of renal cancer cell lines from two major resources enables genomics-guided cell line selection Nat Commun, 8, pp. 15165. doi:10.1038/ncomms15165 (10 May 2017)
Zhai H, Li XM, Liu F, Chen BD, Zheng H, Wang XM, Liao W, Chen QJ, Ma YT, Yang YN. Expression pattern of genome-scale long noncoding RNA following acute myocardial infarction in Chinese Uyghur patients. Oncotarget, 8(19), pp. 31449-31464. doi:10.18632/oncotarget.16355 (9 May 2017)
Walsh RM, Shen EY, Bagot RC, Anselmo A, Jiang Y, Javidfar B, Wojtkiewicz GJ, Cloutier J, Chen JW, Sadreyev R, Nestler EJ, Akbarian S, Hochedlinger K. Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice Nat Commun, 8, pp. 15142. doi:10.1038/ncomms15142 (9 May 2017)
Del Carratore F, Jankevics A, Eisinga R, Heskes T, Hong F, Breitling R. RankProd 2.0: a refactored Bioconductor package for detecting differentially expressed features in molecular profiling datasets. Bioinformatics. doi:10.1093/bioinformatics/btx292 (8 May 2017)
Bender MC, Sifuentes CJ, Denver RJ. Leptin Induces Mitosis and Activates the Canonical Wnt/β-Catenin Signaling Pathway in Neurogenic Regions of Xenopus Tadpole Brain Front Endocrinol (Lausanne), 8, pp. 99. doi:10.3389/fendo.2017.00099 (8 May 2017)
O'Neill K, Hills M, Gottlieb M, Borkowski M, Karsan A, Lansdorp PM. Assembling Draft Genomes using contiBAIT. Bioinformatics. doi:10.1093/bioinformatics/btx281 (5 May 2017)
Chiu A, Ayub M, Dive C, Brady G, Miller CJ. twoddpcr: An R/Bioconductor package and Shiny app for Droplet Digital PCR analysis. Bioinformatics. doi:10.1093/bioinformatics/btx308 (5 May 2017)
Mulvey CM, Breckels LM, Geladaki A, Britovšek NK, Nightingale DJH, Christoforou A, Elzek M, Deery MJ, Gatto L, Lilley KS. Using hyperLOPIT to perform high-resolution mapping of the spatial proteome. Nat Protoc, 12(6), pp. 1110-1135. doi:10.1038/nprot.2017.026 (4 May 2017)


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