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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 2019-11-19T09:20:06-05:00.

Bhuva DD, Cursons J, Smyth GK, Davis MJ. Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer. Genome Biol, 20(1), pp. 236. doi:10.1186/s13059-019-1851-8 (14 November 2019)

Zhang C, Hu X, Qi F, Luo J, Li X. Identification of CD2, CCL5 and CCR5 as potential therapeutic target genes for renal interstitial fibrosis. Ann Transl Med, 7(18), pp. 454. doi:10.21037/atm.2019.08.62 (9 November 2019)

Jiang Y, Zhang H, Andrews SV, Arshad H, Ewart S, Holloway JW, Fallin MD, Bakulski KM, Karmaus W. Estimation of Eosinophil Cells in Cord Blood with References Based on Blood in Adults via Bayesian Measurement Error Modeling. Bioinformatics. doi:10.1093/bioinformatics/btz839 (9 November 2019)

Zheng SC, Breeze CE, Beck S, Dong D, Zhu T, Ma L, Ye W, Zhang G, Teschendorff AE. EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI. Bioinformatics. doi:10.1093/bioinformatics/btz833 (9 November 2019)

Carlucci M, Kriščiūnas A, Li H, Gibas P, Koncevičius K, Petronis A, Oh G. DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity. Bioinformatics. doi:10.1093/bioinformatics/btz834 (8 November 2019)

Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D, Santana-Garcia W, Tan G, Chèneby J, Ballester B, Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. doi:10.1093/nar/gkz1001 (8 November 2019)

Pal K, Tagliaferri I, Livi CM, Ferrari F. HiCBricks: building blocks for efficient handling of large Hi-C datasets. Bioinformatics. doi:10.1093/bioinformatics/btz808 (7 November 2019)

Fraser L, Brym P, Pareek CS, Mogielnicka-Brzozowska M, Paukszto Ł, Jastrzębski JP, Wasilewska-Sakowska K, Mańkowska A, Sobiech P, Żukowski K. Transcriptome analysis of boar spermatozoa with different freezability using RNA-Seq. Theriogenology. doi:10.1016/j.theriogenology.2019.11.001 (2 November 2019)

Kuijjer ML, Hsieh PH, Quackenbush J, Glass K. lionessR: single sample network inference in R. BMC Cancer, 19(1), pp. 1003. doi:10.1186/s12885-019-6235-7 (25 October 2019)

Ibn-Salem J, Andrade-Navarro MA. 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs. BMC Genomics, 20(1), pp. 777. doi:10.1186/s12864-019-6088-0 (25 October 2019)

Gonçalves ANA, Lever M, Russo PST, Gomes-Correia B, Urbanski AH, Pollara G, Noursadeghi M, Maracaja-Coutinho V, Nakaya HI. Assessing the Impact of Sample Heterogeneity on Transcriptome Analysis of Human Diseases Using MDP Webtool. Front Genet, 10, pp. 971. doi:10.3389/fgene.2019.00971 (24 October 2019)

Napolitano F, Carrella D, Gao X, di Bernardo D. gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles. Bioinformatics. doi:10.1093/bioinformatics/btz803 (24 October 2019)

Ma B, Huang Z, Wang Q, Zhang J, Zhou B, Wu J. Integrative analysis of genetic and epigenetic profiling of lung squamous cell carcinoma (LSCC) patients to identify smoking level relevant biomarkers. BioData Min, 12, pp. 18. doi:10.1186/s13040-019-0207-y (21 October 2019)

Wang LG, Lam TT, Xu S, Dai Z, Zhou L, Feng T, Guo P, Dunn CW, Jones BR, Bradley T, Zhu H, Guan Y, Jiang Y, Yu G. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Mol Biol Evol. doi:10.1093/molbev/msz240 (21 October 2019)

Li Y, Fan TWM, Lane AN, Kang WY, Arnold SM, Stromberg AJ, Wang C, Chen L. SDA: a semi-parametric differential abundance analysis method for metabolomics and proteomics data. BMC Bioinformatics, 20(1), pp. 501. doi:10.1186/s12859-019-3067-z (17 October 2019)

Corfitsen HT, Krantz B, Larsen A, Drago A. Molecular pathway analysis associates alterations in obesity-related genes and antipsychotic-induced weight gain. Acta Neuropsychiatr, pp. 1-12. doi:10.1017/neu.2019.41 (17 October 2019)

Reyes ALP, Silva TC, Coetzee SG, Plummer JT, Davis BD, Chen S, Hazelett DJ, Lawrenson K, Berman BP, Gayther SA, Jones MR. GENAVi: a shiny web application for gene expression normalization, analysis and visualization. BMC Genomics, 20(1), pp. 745. doi:10.1186/s12864-019-6073-7 (16 October 2019)

Sepulveda JL. Using R and Bioconductor in Clinical Genomics and Transcriptomics. J Mol Diagn. doi:10.1016/j.jmoldx.2019.08.006 (9 October 2019)

He X, Xu H, Zhao W, Zhan M, Li Y, Liu H, Tan L, Lu L. POPDC3 is a potential biomarker for prognosis and radioresistance in patients with head and neck squamous cell carcinoma. Oncol Lett, 18(5), pp. 5468-5480. doi:10.3892/ol.2019.10888 (19 September 2019)

Noblejas-López MDM, Nieto-Jiménez C, Morcillo García S, Pérez-Peña J, Nuncia-Cantarero M, Andrés-Pretel F, Galán-Moya EM, Amir E, Pandiella A, Győrffy B, Ocana A. Expression of MHC class I, HLA-A and HLA-B identifies immune-activated breast tumors with favorable outcome. Oncoimmunology, 8(10), pp. e1629780. doi:10.1080/2162402X.2019.1629780 (3 July 2019)