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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 2018-08-16T04:20:06-04:00.

Tian L, Su S, Dong X, Amann-Zalcenstein D, Biben C, Seidi A, Hilton DJ, Naik SH, Ritchie ME. scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data. PLoS Comput Biol, 14(8), pp. e1006361. doi:10.1371/journal.pcbi.1006361 (10 August 2018)
Murali A, Bhargava A, Wright ES. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome, 6(1), pp. 140. doi:10.1186/s40168-018-0521-5 (9 August 2018)
Davie K, Janssens J, Koldere D, De Waegeneer M, Pech U, Kreft Ł, Aibar S, Makhzami S, Christiaens V, Bravo González-Blas C, Poovathingal S, Hulselmans G, Spanier KI, Moerman T, Vanspauwen B, Geurs S, Voet T, Lammertyn J, Thienpont B, Liu S, Konstantinides N, Fiers M, Verstreken P, Aerts S. A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain Cell, 174(4), pp. 982-998.e20. doi:10.1016/j.cell.2018.05.057 (9 August 2018)
Wang Y, Wang Z, Xu J, Li J, Li S, Zhang M, Yang D. Systematic identification of non-coding pharmacogenomic landscape in cancer Nat Commun, 9, pp. 3192. doi:10.1038/s41467-018-05495-9 (9 August 2018)
Stark AK, Chandra A, Chakraborty K, Alam R, Carbonaro V, Clark J, Sriskantharajah S, Bradley G, Richter AG, Banham-Hall E, Clatworthy MR, Nejentsev S, Hamblin JN, Hessel EM, Condliffe AM, Okkenhaug K. PI3Kδ hyper-activation promotes development of B cells that exacerbate Streptococcus pneumoniae infection in an antibody-independent manner Nat Commun, 9, pp. 3174. doi:10.1038/s41467-018-05674-8 (9 August 2018)
McDermaid A, Monier B, Zhao J, Liu B, Ma Q. Interpretation of differential gene expression results of RNA-seq data: review and integration. Brief Bioinform. doi:10.1093/bib/bby067 (6 August 2018)
Nguyen B, Venet D, Azim HA Jr, Brown D, Desmedt C, Lambertini M, Majjaj S, Pruneri G, Peccatori F, Piccart M, Rothé F, Sotiriou C. Breast cancer diagnosed during pregnancy is associated with enrichment of non-silent mutations, mismatch repair deficiency signature and mucin mutations NPJ Breast Cancer, 4, pp. 23. doi:10.1038/s41523-018-0077-3 (6 August 2018)
Zhao X, Liang M, Li X, Qiu X, Cui L. Identification of key genes and pathways associated with osteogenic differentiation of adipose stem cells. J Cell Physiol. doi:10.1002/jcp.26943 (5 August 2018)
Fu JM, Leslie EJ, Scott AF, Murray JC, Marazita ML, Beaty TH, Scharpf RB, Ruczinski I. Detection of de novo copy number deletions from targeted sequencing of trios. Bioinformatics. doi:10.1093/bioinformatics/bty677 (2 August 2018)
Hu Z, Jujjavarapu C, Hughey JJ, Andorf S, Lee HC, Gherardini PF, Spitzer MH, Thomas CG, Campbell J, Dunn P, Wiser J, Kidd BA, Dudley JT, Nolan GP, Bhattacharya S, Butte AJ. MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data. Cell Rep, 24(5), pp. 1377-1388. doi:10.1016/j.celrep.2018.07.003 (31 July 2018)
Stansfield JC, Cresswell KG, Vladimirov VI, Dozmorov MG. HiCcompare: an R-package for joint normalization and comparison of HI-C datasets. BMC Bioinformatics, 19(1), pp. 279. doi:10.1186/s12859-018-2288-x (31 July 2018)
Hinojosa AJ, Deogracias R, Rico B. The Microtubule Regulator NEK7 Coordinates the Wiring of Cortical Parvalbumin Interneurons Cell Rep, 24(5), pp. 1231-1242. doi:10.1016/j.celrep.2018.06.115 (31 July 2018)
Raymond-Bouchard I, Tremblay J, Altshuler I, Greer CW, Whyte LG. Comparative Transcriptomics of Cold Growth and Adaptive Features of a Eury- and Steno-Psychrophile Front Microbiol, 9, pp. 1565. doi:10.3389/fmicb.2018.01565 (31 July 2018)
Zhang GL, Song JL, Ji CL, Feng YL, Yu J, Nyachoti CM, Yang GS. Zearalenone Exposure Enhanced the Expression of Tumorigenesis Genes in Donkey Granulosa Cells via the PTEN/PI3K/AKT Signaling Pathway Front Genet, 9, pp. 293. doi:10.3389/fgene.2018.00293 (31 July 2018)
Veskimäe K, Scaravilli M, Niininen W, Karvonen H, Jaatinen S, Nykter M, Visakorpi T, Mäenpää J, Ungureanu D, Staff S. Expression Analysis of Platinum Sensitive and Resistant Epithelial Ovarian Cancer Patient Samples Reveals New Candidates for Targeted Therapies Transl Oncol, 11(5), pp. 1160-1170. doi:10.1016/j.tranon.2018.07.010 (26 July 2018)
Rodriguez-Martinez A, Ayala R, Posma JM, Dumas ME. Exploring the Genetic Landscape of Metabolic Phenotypes with MetaboSignal. Curr Protoc Bioinformatics, 61(1), pp. 14.14.1-14.14.13. doi:10.1002/cpbi.41 (25 July 2018)
Kriss CL, Gregory-Lott E, Storey AJ, Tackett AJ, Wahls WP, Stevens SM Jr. In vivo metabolic tracing demonstrates the site-specific contribution of hepatic ethanol metabolism to histone acetylation. Alcohol Clin Exp Res. doi:10.1111/acer.13843 (21 July 2018)
Gattolliat CH, Couvé S, Meurice G, Oréar C, Droin N, Chiquet M, Ferlicot S, Verkarre V, Vasiliu V, Molinié V, Méjean A, Dessen P, Giraud S, Bressac-De-Paillerets B, Gardie B, Teh BT, Richard S, Gad S. Integrative analysis of dysregulated microRNAs and mRNAs in multiple recurrent synchronized renal tumors from patients with von Hippel-Lindau disease Int J Oncol, 53(4), pp. 1455-1468. doi:10.3892/ijo.2018.4490 (19 July 2018)
Valdeolivas A, Tichit L, Navarro C, Perrin S, Odelin G, Levy N, Cau P, Remy E, Baudot A. Random Walk with Restart on Multiplex and Heterogeneous Biological Networks. Bioinformatics. doi:10.1093/bioinformatics/bty637 (18 July 2018)
Kimes PK, Reyes A. Reproducible and replicable comparisons using SummarizedBenchmark. Bioinformatics. doi:10.1093/bioinformatics/bty627 (17 July 2018)

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