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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 2016-10-20T00:40:10-04:00.

Eikrem OS, Strauss P, Beisland C, Scherer A, Landolt L, Flatberg A, Leh S, Beisvag V, Skogstrand T, Hjelle K, Shresta A, Marti HP. Development and confirmation of potential gene classifiers of human clear cell renal cell carcinoma using next-generation RNA sequencing. Scand J Urol, pp. 1-11. doi:10.1080/21681805.2016.1238007 (14 October 2016)
Dukić M, Berner D, Roesti M, Haag CR, Ebert D. A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna BMC Genet, 17, pp. 137. doi:10.1186/s12863-016-0445-7 (13 October 2016)
Picaud S, Leonards K, Lambert JP, Dovey O, Wells C, Fedorov O, Monteiro O, Fujisawa T, Wang CY, Lingard H, Tallant C, Nikbin N, Guetzoyan L, Ingham R, Ley SV, Brennan P, Muller S, Samsonova A, Gingras AC, Schwaller J, Vassiliou G, Knapp S, Filippakopoulos P. Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia Sci Adv, 2(10), pp. e1600760. doi:10.1126/sciadv.1600760 (12 October 2016)
Paul S, Gayen D, Datta SK, Datta K. Analysis of high iron rice lines reveals new miRNAs that target iron transporters in roots J Exp Bot, 67(19), pp. 5811-5824. doi:10.1093/jxb/erw346 (11 October 2016)
Illingworth RS, Hölzenspies JJ, Roske FV, Bickmore WA, Brickman JM. Polycomb enables primitive endoderm lineage priming in embryonic stem cells eLife, 5, pp. e14926. doi:10.7554/eLife.14926 (10 October 2016)
Noristani HN, Sabourin JC, Boukhaddaoui H, Chan-Seng E, Gerber YN, Perrin FE. Spinal cord injury induces astroglial conversion towards neuronal lineage Mol Neurodegener, 11, pp. 68. doi:10.1186/s13024-016-0133-0 (6 October 2016)
Wang Y, Zhao W, Zhou X. Matrix factorization reveals aging-specific co-expression gene modules in the fat and muscle tissues in nonhuman primates Sci Rep, 6, pp. 34335. doi:10.1038/srep34335 (5 October 2016)
Samaras A, Dimitroglou A, Sarropoulou E, Papaharisis L, Kottaras L, Pavlidis M. Repeatability of cortisol stress response in the European sea bass (Dicentrarchus labrax) and transcription differences between individuals with divergent responses Sci Rep, 6, pp. 34858. doi:10.1038/srep34858 (5 October 2016)
Flores-Pérez A, Marchat LA, Rodríguez-Cuevas S, Bautista-Piña V, Hidalgo-Miranda A, Ocampo EA, Martínez MS, Palma-Flores C, Fonseca-Sánchez MA, Astudillo-de la Vega H, Ruíz-García E, González-Barrios JA, Pérez-Plasencia C, Streber ML, López-Camarillo C. Dual targeting of ANGPT1 and TGFBR2 genes by miR-204 controls angiogenesis in breast cancer Sci Rep, 6, pp. 34504. doi:10.1038/srep34504 (5 October 2016)
Džunková M, D'Auria G, Xu H, Huang J, Duan Y, Moya A, Kelly CP, Chen X. The Monoclonal Antitoxin Antibodies (Actoxumab–Bezlotoxumab) Treatment Facilitates Normalization of the Gut Microbiota of Mice with Clostridium difficile Infection Front Cell Infect Microbiol, 6, pp. 119. doi:10.3389/fcimb.2016.00119 (4 October 2016)
Yalamanchili N, Kriete A, Alfego D, Danowski KM, Kari C, Rodeck U. Distinct Cell Stress Responses Induced by ATP Restriction in Quiescent Human Fibroblasts Front Genet, 7, pp. 171. doi:10.3389/fgene.2016.00171 (4 October 2016)
Alhamdoosh M, Ng M, Wilson NJ, Sheridan JM, Huynh H, Wilson MJ, Ritchie ME. Combining multiple tools outperforms individual methods in gene set enrichment analyses. Bioinformatics. doi:10.1093/bioinformatics/btw623 (30 September 2016)
Duan Y, Zhou M, Xiao J, Wu C, Zhou L, Zhou F, Du C, Song Y. Prediction of key genes and miRNAs responsible for loss of muscle force in patients during an acute exacerbation of chronic obstructive pulmonary disease Int J Mol Med, 38(5), pp. 1450-1462. doi:10.3892/ijmm.2016.2761 (30 September 2016)
Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE. Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Res. doi:10.1093/nar/gkw852 (29 September 2016)
Love MI, Hogenesch JB, Irizarry RA. Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nat Biotechnol. doi:10.1038/nbt.3682 (26 September 2016)
Liu Y, Wang L, Wang B, Yue M, Cheng Y. Pathway Analysis Based on Attractor and Cross Talk in Colon Cancer Dis Markers, 2016, pp. 2619828. doi:10.1155/2016/2619828 (25 September 2016)
Chen H, Lau MC, Wong MT, Newell EW, Poidinger M, Chen J. Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline. PLoS Comput Biol, 12(9), pp. e1005112. doi:10.1371/journal.pcbi.1005112 (23 September 2016)
Van Leene J, Blomme J, Kulkarni SR, Cannoot B, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Vercruysse L, Vanden Bossche R, Heyndrickx KS, Vanneste S, Goossens A, Gevaert K, Vandepoele K, Gonzalez N, Inzé D, De Jaeger G. Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development J Exp Bot, 67(19), pp. 5825-5840. doi:10.1093/jxb/erw347 (22 September 2016)
Liu P, Jiang W, Zhou S, Gao J, Zhang H. Combined Analysis of ChIP Sequencing and Gene Expression Dataset in Breast Cancer. Pathol Oncol Res. doi:10.1007/s12253-016-0116-z (21 September 2016)


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