Publications

Bioconductor F1000 Research Channel launched!

Featured

Ramos, M, et al. (2017) Software for the Integration of Multiomics Experiments in Bioconductor Cancer Research 77:e39-e42. doi:10.1158/0008-5472.CAN-17-0344
Pasolli, E, et al. (2017) Accessible, curated metagenomic data through ExperimentHub Nature Methods 14, 1023–1024. doi:10.1038/nmeth.4468
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).
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
Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2018-12-15T13:00:10-05:00.

Finak G, Jiang W, Gottardo R. CytoML for cross-platform cytometry data sharing. Cytometry A, 93(12), pp. 1189-1196. doi:10.1002/cyto.a.23663 (15 December 2018)
Wu R, Ruan J, Sun Y, Liu M, Sha Z, Fan C, Wu Q. Long non-coding RNA HIF1A-AS2 facilitates adipose-derived stem cells (ASCs) osteogenic differentiation through miR-665/IL6 axis via PI3K/Akt signaling pathway. Stem Cell Res Ther, 9(1), pp. 348. doi:10.1186/s13287-018-1082-z (13 December 2018)
Trojan SE, Piwowar M, Ostrowska B, Laidler P, Kocemba-Pilarczyk KA. Analysis of Malignant Melanoma Cell Lines Exposed to Hypoxia Reveals the Importance of PFKFB4 Overexpression for Disease Progression. Anticancer Res, 38(12), pp. 6745-6752. doi:10.21873/anticanres.13044 (7 December 2018)
Li GX, Ding ZY, Wang YW, Liu TT, Chen WX, Wu JJ, Xu WQ, Zhu P, Zhang BX. Integrative analysis of DNA methylation and gene expression identify a six epigenetic driver signature for predicting prognosis in hepatocellular carcinoma. J Cell Physiol. doi:10.1002/jcp.27882 (7 December 2018)
Yu G, Lam TT, Zhu H, Guan Y. Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree. Mol Biol Evol, 35(12), pp. 3041-3043. doi:10.1093/molbev/msy194 (1 December 2018)
Sherman T, Fu J, Scharpf RB, Bureau A, Ruczinski I. Detection of rare disease variants in extended pedigrees using RVS. Bioinformatics. doi:10.1093/bioinformatics/bty976 (30 November 2018)
Naake T, Fernie AR. MetNet: Metabolite network prediction from high-resolution mass spectrometry data in R aids metabolite annotation. Anal Chem. doi:10.1021/acs.analchem.8b04096 (30 November 2018)
Kaisers W, Schwender H, Schaal H. Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities. Int J Mol Sci, 19(11). doi:10.3390/ijms19113687 (21 November 2018)
Kruthika BS, Jain R, Arivazhagan A, Bharath RD, Yasha TC, Kondaiah P, Santosh V. Transcriptome profiling reveals PDZ binding kinase as a novel biomarker in peritumoral brain zone of glioblastoma. J Neurooncol. doi:10.1007/s11060-018-03051-5 (20 November 2018)
Dogu E, Mohammad Taheri S, Olivella R, Marty F, Lienert I, Reiter L, Sabidó E, Vitek O. MSstatsQC 2.0: R/Bioconductor package for statistical quality control of mass spectrometry-based proteomic experiments. J Proteome Res. doi:10.1021/acs.jproteome.8b00732 (19 November 2018)
Raborn RT, Brendel VP. Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes. Methods Mol Biol, 1858, pp. 99-116. doi:10.1007/978-1-4939-8775-7_9 (11 November 2018)
Foroutan M, Bhuva DD, Lyu R, Horan K, Cursons J, Davis MJ. Single sample scoring of molecular phenotypes. BMC Bioinformatics, 19(1), pp. 404. doi:10.1186/s12859-018-2435-4 (6 November 2018)
Rizvi AA, Karaesmen E, Morgan M, Preus L, Wang J, Sovic M, Hahn T, Sucheston-Campbell LE. gwasurvivr : an R package for genome wide survival analysis. Bioinformatics. doi:10.1093/bioinformatics/bty920 (5 November 2018)
Zhu A, Ibrahim JG, Love MI. Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics. doi:10.1093/bioinformatics/bty895 (3 November 2018)
Lee LH, Halu A, Morgan S, Iwata H, Aikawa M, Singh SA. XINA: A Workflow for the Integration of Multiplexed Proteomics Kinetics Data with Network Analysis. J Proteome Res. doi:10.1021/acs.jproteome.8b00615 (29 October 2018)
Silva TC, Coetzee SG, Gull N, Yao L, Hazelett DJ, Noushmehr H, Lin DC, Berman BP. ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. Bioinformatics. doi:10.1093/bioinformatics/bty902 (26 October 2018)
Beyrend G, Stam K, Höllt T, Ossendorp F, Arens R. Cytofast: A workflow for visual and quantitative analysis of flow and mass cytometry data to discover immune signatures and correlations. Comput Struct Biotechnol J, 16, pp. 435-442. doi:10.1016/j.csbj.2018.10.004 (24 October 2018)
Rodriguez-Martinez A, Ayala R, Posma JM, Harvey N, Jiménez B, Sonomura K, Sato TA, Matsuda F, Zalloua P, Gauguier D, Nicholson JK, Dumas ME. pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra. Bioinformatics. doi:10.1093/bioinformatics/bty837 (23 October 2018)
Davis S, Ramos M, Shepherd L, Turaga N, Geistlinger L, Morgan MT, Haibe-Kains B, Waldron L. Orchestrating a community-developed computational workshop and accompanying training materials. F1000Res, 7, pp. 1656. doi:10.12688/f1000research.16516.1 (17 October 2018)
Love MI, Soneson C, Patro R. Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification. F1000Res, 7, pp. 952. doi:10.12688/f1000research.15398.3 (27 June 2018)

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.

Packages »

Bioconductor's stable, semi-annual release:

Bioconductor is also available via Docker and Amazon Machine Images.