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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

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2016-09-26T19:20:09-04:00.

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)
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)
H Backman TW, Girke T. systemPipeR: NGS workflow and report generation environment. BMC Bioinformatics, 17, pp. 388. doi:10.1186/s12859-016-1241-0 (20 September 2016)
Bermick JR, Lambrecht NJ, denDekker AD, Kunkel SL, Lukacs NW, Hogaboam CM, Schaller MA. Neonatal monocytes exhibit a unique histone modification landscape Clin Epigenetics, 8, pp. 99. doi:10.1186/s13148-016-0265-7 (20 September 2016)
Toropainen S, Niskanen EA, Malinen M, Sutinen P, Kaikkonen MU, Palvimo JJ. Global analysis of transcription in castration-resistant prostate cancer cells uncovers active enhancers and direct androgen receptor targets Sci Rep, 6, pp. 33510. doi:10.1038/srep33510 (19 September 2016)
Wang X, Zhang L, Li H, Sun W, Zhang H, Lai M. THBS2 is a Potential Prognostic Biomarker in Colorectal Cancer Sci Rep, 6, pp. 33366. doi:10.1038/srep33366 (16 September 2016)
Cao Z, Zhang S. An integrative and comparative study of pan-cancer transcriptomes reveals distinct cancer common and specific signatures Sci Rep, 6, pp. 33398. doi:10.1038/srep33398 (16 September 2016)
Sen S, Block KF, Pasini A, Baylin SB, Easwaran H. Genome-wide positioning of bivalent mononucleosomes BMC Med Genomics, 9, pp. 60. doi:10.1186/s12920-016-0221-6 (15 September 2016)
Müller L, Gerighausen D, Farman M, Zeckzer D. Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering BMC Bioinformatics, 17, pp. 377. doi:10.1186/s12859-016-1248-6 (15 September 2016)
Käser-Pébernard S, Pfefferli C, Aschinger C, Wicky C. Fine-tuning of chromatin composition and Polycomb recruitment by two Mi2 homologues during C. elegans early embryonic development Epigenetics Chromatin, 9, pp. 39. doi:10.1186/s13072-016-0091-3 (15 September 2016)
Dheilly E, Gall SL, Guillou MC, Renou JP, Bonnin E, Orsel M, Lahaye M. Cell wall dynamics during apple development and storage involves hemicellulose modifications and related expressed genes BMC Plant Biol, 16, pp. 201. doi:10.1186/s12870-016-0887-0 (15 September 2016)
Geybels MS, Wright JL, Bibikova M, Klotzle B, Fan JB, Zhao S, Feng Z, Ostrander EA, Lin DW, Nelson PS, Stanford JL. Epigenetic signature of Gleason score and prostate cancer recurrence after radical prostatectomy Clin Epigenetics, 8, pp. 97. doi:10.1186/s13148-016-0260-z (15 September 2016)
Fu XL, Liu DJ, Yan TT, Yang JY, Yang MW, Li J, Huo YM, Liu W, Zhang JF, Hong J, Hua R, Chen HY, Sun YW. Analysis of long non-coding RNA expression profiles in pancreatic ductal adenocarcinoma Sci Rep, 6, pp. 33535. doi:10.1038/srep33535 (15 September 2016)
Basu S, Hadzhiev Y, Petrosino G, Nepal C, Gehrig J, Armant O, Ferg M, Strahle U, Sanges R, Müller F. The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome Sci Rep, 6, pp. 33210. doi:10.1038/srep33210 (15 September 2016)
Zheng J, Harris MR, Masci AM, Lin Y, Hero A, Smith B, He Y. The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis J Biomed Semantics, 7, pp. 53. doi:10.1186/s13326-016-0100-2 (14 September 2016)
Zhu J, Deane NG, Lewis KB, Padmanabhan C, Washington MK, Ciombor KK, Timmers C, Goldberg RM, Beauchamp RD, Chen X. Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples Sci Rep, 6, pp. 33273. doi:10.1038/srep33273 (14 September 2016)
Wilson S, Qi J, Filipp FV. Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines Sci Rep, 6, pp. 32611. doi:10.1038/srep32611 (14 September 2016)
duVerle DA, Yotsukura S, Nomura S, Aburatani H, Tsuda K. CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. BMC Bioinformatics, 17(1), pp. 363. doi:10.1186/s12859-016-1175-6 (13 September 2016)
Dong K, Zhao H, Tong T, Wan X. NBLDA: negative binomial linear discriminant analysis for RNA-Seq data BMC Bioinformatics, 17(1), pp. 369. doi:10.1186/s12859-016-1208-1 (13 September 2016)
Chen X, Chakravarty T, Zhang Y, Li X, Zhong JF, Wang C. Single-cell transcriptome and epigenomic reprogramming of cardiomyocyte-derived cardiac progenitor cells Sci Data, 3, pp. 160079. doi:10.1038/sdata.2016.79 (13 September 2016)

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