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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 2019-10-22T02:40:06-04:00.

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. 1-21. 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)
Thodberg M, Thieffry A, Vitting-Seerup K, Andersson R, Sandelin A. CAGEfightR: analysis of 5'-end data using R/Bioconductor. BMC Bioinformatics, 20(1), pp. 487. doi:10.1186/s12859-019-3029-5 (4 October 2019)
Stanstrup J, Broeckling CD, Helmus R, Hoffmann N, Mathé E, Naake T, Nicolotti L, Peters K, Rainer J, Salek RM, Schulze T, Schymanski EL, Stravs MA, Thévenot EA, Treutler H, Weber RJM, Willighagen E, Witting M, Neumann S. The metaRbolomics Toolbox in Bioconductor and beyond. Metabolites, 9(10). doi:10.3390/metabo9100200 (23 September 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)
Korandla DR, Wozniak JM, Campeau A, Gonzalez DJ, Wright ES. AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions. Bioinformatics. doi:10.1093/bioinformatics/btz714 (18 September 2019)
Bais AS, Kostka D. scds: Computational Annotation of Doublets in Single-Cell RNA Sequencing Data. Bioinformatics. doi:10.1093/bioinformatics/btz698 (10 September 2019)
Tran AN, Dussaq AM, Kennell T Jr, Willey CD, Hjelmeland AB. HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data. BMC Bioinformatics, 20(1), pp. 463. doi:10.1186/s12859-019-3059-z (9 September 2019)
Li Z, Wu H. TOAST: improving reference-free cell composition estimation by cross-cell type differential analysis. Genome Biol, 20(1), pp. 190. doi:10.1186/s13059-019-1778-0 (4 September 2019)
Ceddia G, Martino LN, Parodi A, Secchi P, Campaner S, Masseroli M. Association rule mining to identify transcription factor interactions in genomic regions. Bioinformatics. doi:10.1093/bioinformatics/btz687 (3 September 2019)
Schumann F, Blanc E, Messerschmidt C, Blankenstein T, Busse A, Beule D. SigsPack, a package for cancer mutational signatures. BMC Bioinformatics, 20(1), pp. 450. doi:10.1186/s12859-019-3043-7 (2 September 2019)
Lin Y, Ghazanfar S, Strbenac D, Wang A, Patrick E, Lin DM, Speed T, Yang JYH, Yang P. Evaluating stably expressed genes in single cells. Gigascience, 8(9). doi:10.1093/gigascience/giz106 (1 September 2019)
Porubsky D, Sanders AD, Taudt A, Colomé-Tatché M, Lansdorp PM, Guryev V. breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data. Bioinformatics. doi:10.1093/bioinformatics/btz681 (30 August 2019)
Xu T, Jin P, Qin Z. Regulatory annotation of genomic intervals based on tissue-specific expression QTLs. Bioinformatics. doi:10.1093/bioinformatics/btz669 (27 August 2019)
Sánchez-Pla A, Salicrú M, Ocaña J. An equivalence approach to the integrative analysis of feature lists. BMC Bioinformatics, 20(1), pp. 441. doi:10.1186/s12859-019-3008-x (27 August 2019)
Tan G, Polychronopoulos D, Lenhard B. CNEr: A toolkit for exploring extreme noncoding conservation. PLoS Comput Biol, 15(8), pp. e1006940. doi:10.1371/journal.pcbi.1006940 (26 August 2019)
Zhou D, Sun Y, Jia Y, Liu D, Wang J, Chen X, Zhang Y, Ma X. Bioinformatics and functional analyses of key genes in smoking-associated lung adenocarcinoma. Oncol Lett, 18(4), pp. 3613-3622. doi:10.3892/ol.2019.10733 (7 August 2019)
List M, Dehghani Amirabad A, Kostka D, Schulz MH. Large-scale inference of competing endogenous RNA networks with sparse partial correlation. Bioinformatics, 35(14), pp. i596-i604. doi:10.1093/bioinformatics/btz314 (15 July 2019)

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