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 2015-01-27T01:10:18-08:00.

Yang ZH, Zheng R, Gao Y, Zhang Q. Identification of suitable genes contributes to lung adenocarcinoma clustering by multiple meta-analysis methods. Clin Respir J. doi:10.1111/crj.12271 (26 January 2015)
Nowak MD, Russo G, Schlapbach R, Huu CN, Lenhard M, Conti E. The draft genome of Primula veris yields insights into the molecular basis of heterostyly Genome Biol, 16(1), pp. 12. doi:10.1186/s13059-014-0567-z (24 January 2015)
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)
Shen Y, Rahman M, Piccolo SR, Gusenleitner D, Ei-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE. ASSIGN: Context-specific Genomic Profiling of Multiple Heterogeneous Biological Pathways. Bioinformatics. doi:10.1093/bioinformatics/btv031 (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)
Wheeler NJ, Agbedanu PN, Kimber MJ, Ribeiro P, Day TA, Zamanian M. Functional analysis of Girardia tigrina transcriptome seeds pipeline for anthelmintic target discovery Parasit Vectors, 8(1), pp. 34. doi:10.1186/s13071-014-0622-3 (20 January 2015)
Gevaert O. MethylMix: an R package for identifying DNA methylation driven genes. Bioinformatics. doi:10.1093/bioinformatics/btv020 (20 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)
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)
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)
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)
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)
Barriocanal M, Carnero E, Segura V, Fortes P. Long Non-Coding RNA BST2/BISPR is Induced by IFN and Regulates the Expression of the Antiviral Factor Tetherin Front Immunol, 5, pp. 655. doi:10.3389/fimmu.2014.00655 (9 January 2015)
Capurro A, Bodea LG, Schaefer P, Luthi-Carter R, Perreau VM. Computational deconvolution of genome wide expression data from Parkinson's and Huntington's disease brain tissues using population-specific expression analysis Front Neurosci, 8, pp. 441. doi:10.3389/fnins.2014.00441 (9 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)
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)
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)
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)

Books

Monograph     R Programming for Bioinformatics     Bioconductor Case Studies

Book Chapters

Technical Reports and Working Papers

Compendia

Literature Search »

 

Courses & Conferences »

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

Bioconductor Release »

Packages in the stable, semi-annual release:


Bioconductor is also available as an Amazon Machine Image and a series of Docker images.
Fred Hutchinson Cancer Research Center