Publications

Featured

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, and Smyth, GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies Nucl. Acids Res; doi: 10.1093/nar/gkv007
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
Tippmann, S. (2015) Programming tools: Adventures with R. Nature 517: 109–110.
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
Lawrence, M, and Morgan, M. (2014) Scalable Genomics with R and Bioconductor Statistical Science, Vol. 29, No. 2, 214-226 10.1214/14-STS476

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2015-01-26T01:00:08-08:00.

Benton MC, Johnstone A, Eccles D, Harmon B, Hayes MT, Lea RA, Griffiths L, Hoffman EP, Stubbs RS, Macartney-Coxson D. An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss Genome Biol, 16(1), pp. 8. doi:10.1186/s13059-014-0569-x (22 January 2015)
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. doi:10.1093/nar/gkv007 (20 January 2015)
Gevaert O. MethylMix: an R package for identifying DNA methylation driven genes. Bioinformatics. doi:10.1093/bioinformatics/btv020 (20 January 2015)
O'Neill K, Aghaeepour N, Parker J, Hogge D, Karsan A, Dalal B, Brinkman RR. Deep profiling of multitube flow cytometry data. Bioinformatics. doi:10.1093/bioinformatics/btv008 (18 January 2015)
Aibar S, Fontanillo C, Droste C, De Las Rivas J. Functional Gene Networks: R/Bioc package to generate and analyze gene networks derived from functional enrichment and clustering. Bioinformatics. doi:10.1093/bioinformatics/btu864 (18 January 2015)
Wang X, Wen J, Li R, Qiu G, Zhou L, Wen X. Gene expression profiling analysis of castration-resistant prostate cancer. Med Sci Monit, 21, pp. 205-12. doi:10.12659/MSM.891193 (16 January 2015)
Obulkasim A, Meijer GA, van de Wiel MA. Semi-supervised adaptive-height snipping of the hierarchical clustering tree. BMC Bioinformatics, 16(1), pp. 15. doi:10.1186/s12859-014-0448-1 (16 January 2015)
Avican K, Fahlgren A, Huss M, Heroven AK, Beckstette M, Dersch P, Fällman M. Reprogramming of Yersinia from Virulent to Persistent Mode Revealed by Complex In Vivo RNA-seq Analysis PLoS Pathog, 11(1), pp. e1004600. doi:10.1371/journal.ppat.1004600 (15 January 2015)
Morrow JD, Qiu W, Chhabra D, Rennard SI, Belloni P, Belousov A, Pillai SG, Hersh CP. Identifying a gene expression signature of frequent COPD exacerbations in peripheral blood using network methods BMC Med Genomics, 8(1), pp. 1. doi:10.1186/s12920-014-0072-y (13 January 2015)
Tonner PD, Pittman AM, Gulli JG, Sharma K, Schmid AK. A Regulatory Hierarchy Controls the Dynamic Transcriptional Response to Extreme Oxidative Stress in Archaea PLoS Genet, 11(1), pp. e1004912. doi:10.1371/journal.pgen.1004912 (8 January 2015)
Van Gassen S, Callebaut B, Van Helden MJ, Lambrecht BN, Demeester P, Dhaene T, Saeys Y. FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data. Cytometry A. doi:10.1002/cyto.a.22625 (8 January 2015)
Yoo S, Takikawa S, Geraghty P, Argmann C, Campbell J, Lin L, Huang T, Tu Z, Feronjy R, Spira A, Schadt EE, Powell CA, Zhu J. Integrative Analysis of DNA Methylation and Gene Expression Data Identifies EPAS1 as a Key Regulator of COPD PLoS Genet, 11(1), pp. e1004898. doi:10.1371/journal.pgen.1004898 (8 January 2015)
Jang JC, Chen G, Wang SH, Barnes MA, Chung JI, Camberis M, Le Gros G, Cooper PJ, Steel C, Nutman TB, Lazar MA, Nair MG. Macrophage-Derived Human Resistin Is Induced in Multiple Helminth Infections and Promotes Inflammatory Monocytes and Increased Parasite Burden PLoS Pathog, 11(1), pp. e1004579. doi:10.1371/journal.ppat.1004579 (8 January 2015)
Ranjan A, Townsley BT, Ichihashi Y, Sinha NR, Chitwood DH. An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifolia PLoS Genet, 11(1), pp. e1004900. doi:10.1371/journal.pgen.1004900 (8 January 2015)
Kershaw CJ, Costello JL, Castelli LM, Talavera D, Rowe W, Sims PF, Ashe MP, Hubbard SJ, Pavitt GD, Grant CM. The Yeast La Related Protein Slf1p Is a Key Activator of Translation during the Oxidative Stress Response PLoS Genet, 11(1), pp. e1004903. doi:10.1371/journal.pgen.1004903 (8 January 2015)
de la Rica L, García-Gómez A, Comet NR, Rodríguez-Ubreva J, Ciudad L, Vento-Tormo R, Company C, Álvarez-Errico D, García M, Gómez-Vaquero C, Ballestar E. NF-κB-direct activation of microRNAs with repressive effects on monocyte-specific genes is critical for osteoclast differentiation Genome Biol, 16(1), pp. 2. doi:10.1186/s13059-014-0561-5 (5 January 2015)
Costello J, Castelli LM, Rowe W, Kershaw CJ, Talavera D, Mohammad-Qureshi SS, Sims PF, Grant CM, Pavitt GD, Hubbard SJ, Ashe MP. Global mRNA selection mechanisms for translation initiation Genome Biol, 16(1), pp. 10. doi:10.1186/s13059-014-0559-z (5 January 2015)
Roessler S, Lin G, Forgues M, Budhu A, Hoover S, Simpson RM, Wu X, He P, Qin LX, Tang ZY, Ye QH, Wang XW. Integrative Genomic and Transcriptomic Characterization of Matched Primary and Metastatic Liver and Colorectal Carcinoma Int J Biol Sci, 11(1), pp. 88-98. doi:10.7150/ijbs.10583 (1 January 2015)
Wang J, Zuo Y, Man YG, Avital I, Stojadinovic A, Liu M, Yang X, Varghese RS, Tadesse MG, Ressom HW. Pathway and Network Approaches for Identification of Cancer Signature Markers from Omics Data J Cancer, 6(1), pp. 54-65. doi:10.7150/jca.10631 (1 January 2015)
Caiazzo M, Giannelli S, Valente P, Lignani G, Carissimo A, Sessa A, Colasante G, Bartolomeo R, Massimino L, Ferroni S, Settembre C, Benfenati F, Broccoli V. Direct Conversion of Fibroblasts into Functional Astrocytes by Defined Transcription Factors Stem Cell Reports, 4(1), pp. 25-36. doi:10.1016/j.stemcr.2014.12.002 (31 December 2014)

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