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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 2017-01-22T01:20:07-05:00.

Wijetunga NA, Johnston AD, Maekawa R, Delahaye F, Ulahannan N, Kim K, Greally JM. SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. BMC Bioinformatics, 18(1), pp. 41. doi:10.1186/s12859-017-1477-3 (18 January 2017)
Hernandez-Ferrer C, Ruiz-Arenas C, Beltran-Gomila A, González JR. MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration. BMC Bioinformatics, 18(1), pp. 36. doi:10.1186/s12859-016-1455-1 (17 January 2017)
Liu C, Liu Y, Zhang W, Liu X. Screening for potential genes associated with bone overgrowth after mid-shaft femur fracture in a rat model J Orthop Surg Res, 12, pp. 8. doi:10.1186/s13018-017-0510-6 (17 January 2017)
Shah V, Nowinski S, Levi D, Shinomiya I, Kebaier Ep Chaabouni N, Gillett C, Grigoriadis A, Graham TA, Roylance R, Simpson MA, Pinder SE, Sawyer EJ. PIK3CA mutations are common in lobular carcinoma in situ, but are not a biomarker of progression Breast Cancer Res, 19, pp. 7. doi:10.1186/s13058-016-0789-y (17 January 2017)
Furrer R, Eisele PS, Schmidt A, Beer M, Handschin C. Paracrine cross-talk between skeletal muscle and macrophages in exercise by PGC-1α-controlled BNP Sci Rep, 7, pp. 40789. doi:10.1038/srep40789 (16 January 2017)
Gómez-Díaz E, Yerbanga RS, Lefèvre T, Cohuet A, Rowley MJ, Ouedraogo JB, Corces VG. Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae Sci Rep, 7, pp. 40655. doi:10.1038/srep40655 (16 January 2017)
McCarthy DJ, Campbell KR, Lun AT, Wills QF. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics. doi:10.1093/bioinformatics/btw777 (14 January 2017)
Lai YP, Wang LB, Wang WA, Lai LC, Tsai MH, Lu TP, Chuang EY. iGC-an integrated analysis package of gene expression and copy number alteration. BMC Bioinformatics, 18(1), pp. 35. doi:10.1186/s12859-016-1438-2 (14 January 2017)
Novianti PW, Snoek BC, Wilting SM, van de Wiel MA. Better diagnostic signatures from RNAseq data through use of auxiliary co-data. Bioinformatics. doi:10.1093/bioinformatics/btw837 (10 January 2017)
Koper A, Zeef LA, Joseph L, Kerr K, Gosney J, Lindsay MA, Booton R. Whole Transcriptome Analysis of Pre-invasive and Invasive Early Squamous Lung Carcinoma in Archival Laser Microdissected Samples. Respir Res, 18(1), pp. 12. doi:10.1186/s12931-016-0496-3 (10 January 2017)
Ivamoto ST, Reis O Júnior, Domingues DS, dos Santos TB, de Oliveira FF, Pot D, Leroy T, Vieira LG, Carazzolle MF, Pereira GA, Pereira LF. Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis PLoS One, 12(1), pp. e0169595. doi:10.1371/journal.pone.0169595 (9 January 2017)
Rau A, Maugis-Rabusseau C. Transformation and model choice for RNA-seq co-expression analysis. Brief Bioinform. doi:10.1093/bib/bbw128 (8 January 2017)
Fresno C, González GA, Merino GA, Flesia AG, Podhajcer OL, Llera AS, Fernández EA. A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm. Bioinformatics. doi:10.1093/bioinformatics/btw704 (6 January 2017)
Jabbari K, Bernardi G. An Isochore Framework Underlies Chromatin Architecture PLoS One, 12(1), pp. e0168023. doi:10.1371/journal.pone.0168023 (6 January 2017)
Shankar RD, Bhattacharya S, Jujjavarapu C, Andorf S, Wiser JA, Butte AJ. RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data. Bioinformatics. doi:10.1093/bioinformatics/btw719 (5 January 2017)
Pedersen TL, Nookaew I, Wayne Ussery D, Månsson M. PanViz: interactive visualization of the structure of functionally annotated pangenomes. Bioinformatics. doi:10.1093/bioinformatics/btw761 (5 January 2017)
Zacher B, Michel M, Schwalb B, Cramer P, Tresch A, Gagneur J. Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN PLoS One, 12(1), pp. e0169249. doi:10.1371/journal.pone.0169249 (5 January 2017)
Hamilton SL, Logan CA, Fennie HW, Sogard SM, Barry JP, Makukhov AD, Tobosa LR, Boyer K, Lovera CF, Bernardi G. Species-Specific Responses of Juvenile Rockfish to Elevated pCO2: From Behavior to Genomics PLoS One, 12(1), pp. e0169670. doi:10.1371/journal.pone.0169670 (5 January 2017)
Beisser D, Kaschani F, Graupner N, Grossmann L, Jensen M, Ninck S, Schulz F, Rahmann S, Boenigk J, Kaiser M. Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis PLoS One, 12(1), pp. e0168183. doi:10.1371/journal.pone.0168183 (5 January 2017)


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