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Amezquita, R.A., Lun, A.T.L., Becht, E. et al. Orchestrating single-cell analysis with Bioconductor. Nature Methods (2019) doi:10.1038/s41592-019-0654-x
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.

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20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2020-11-28T16:00:10-05:00.

Han Y, Liu X, Ye H, Tian Y, Ji Z. Lower mutant-allele tumor heterogeneity is a biomarker in FGFR3-mutant bladder cancer for better prognosis. World J Surg Oncol, 18(1), pp. 310. doi:10.1186/s12957-020-02084-3 (26 November 2020)
Sherina V, McMurray HR, Powers W, Land H, Love TMT, McCall MN. Multiple imputation and direct estimation for qPCR data with non-detects. BMC Bioinformatics, 21(1), pp. 545. doi:10.1186/s12859-020-03807-9 (26 November 2020)
Munz M, Wohlers I, Simon E, Reinberger T, Busch H, Schaefer AS, Erdmann J. Qtlizer: comprehensive QTL annotation of GWAS results. Sci Rep, 10(1), pp. 20417. doi:10.1038/s41598-020-75770-7 (24 November 2020)
Zhytnik L, Maasalu K, Reimann E, Märtson A, Kõks S. RNA sequencing analysis reveals increased expression of interferon signaling genes and dysregulation of bone metabolism affecting pathways in the whole blood of patients with osteogenesis imperfecta. BMC Med Genomics, 13(1), pp. 177. doi:10.1186/s12920-020-00825-7 (23 November 2020)
Aishwarya S, Gunasekaran K, Margret AA. Computational gene expression profiling in the exploration of biomarkers, non-coding functional RNAs and drug perturbagens for COVID-19. J Biomol Struct Dyn, pp. 1-16. doi:10.1080/07391102.2020.1850360 (23 November 2020)
González JR, López-Sánchez M, Cáceres A, Puig P, Esko T, Pérez-Jurado LA. MADloy: robust detection of mosaic loss of chromosome Y from genotype-array-intensity data. BMC Bioinformatics, 21(1), pp. 533. doi:10.1186/s12859-020-03768-z (23 November 2020)
Hübschmann D, Jopp-Saile L, Andresen C, Krämer S, Gu Z, Heilig CE, Kreutzfeldt S, Teleanu V, Fröhling S, Eils R, Schlesner M. Analysis of Mutational Signatures with YAPSA (Yet Another Package for Signature Analysis). Genes Chromosomes Cancer. doi:10.1002/gcc.22918 (22 November 2020)
Kurzawa N, Becher I, Sridharan S, Franken H, Mateus A, Anders S, Bantscheff M, Huber W, Savitski MM. A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles. Nat Commun, 11(1), pp. 5783. doi:10.1038/s41467-020-19529-8 (13 November 2020)
Su S, Kong W, Zhang J, Wang X, Guo H. Integrated analysis of DNA methylation and gene expression profiles identified S100A9 as a potential biomarker in ulcerative colitis. Biosci Rep. doi:10.1042/BSR20202384 (13 November 2020)
Chen X, Zheng J, Zhuo ML, Zhang A, You Z. A six-gene-based signature for breast cancer radiotherapy sensitivity estimation. Biosci Rep. doi:10.1042/BSR20202376 (12 November 2020)
Prompsy P, Kirchmeier P, Marsolier J, Deloger M, Servant N, Vallot C. Interactive analysis of single-cell epigenomic landscapes with ChromSCape. Nat Commun, 11(1), pp. 5702. doi:10.1038/s41467-020-19542-x (11 November 2020)
Ou J, Liu H, Nirala NK, Stukalov A, Acharya U, Green MR, Zhu LJ. dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data. PLoS One, 15(11), pp. e0242030. doi:10.1371/journal.pone.0242030 (6 November 2020)
Smolander J, Junttila S, Venäläinen MS, Elo LL. ILoReg: a tool for high-resolution cell population identification from single-cell RNA-seq data. Bioinformatics. doi:10.1093/bioinformatics/btaa919 (5 November 2020)
Liu EM, Luna A, Dong G, Sander C. netboxr: Automated discovery of biological process modules by network analysis in R. PLoS One, 15(11), pp. e0234669. doi:10.1371/journal.pone.0234669 (2 November 2020)
Zhang W, Wu H, Li Z. Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach. Bioinformatics. doi:10.1093/bioinformatics/btaa930 (2 November 2020)
Ramos M, Geistlinger L, Oh S, Schiffer L, Azhar R, Kodali H, de Bruijn I, Gao J, Carey VJ, Morgan M, Waldron L. Multiomic Integration of Public Oncology Databases in Bioconductor. JCO Clin Cancer Inform, 4, pp. 958-971. doi:10.1200/CCI.19.00119 (30 October 2020)
Del Barrio E, Inouzhe H, Loubes JM, Matrán C, Mayo-Íscar A. optimalFlow: optimal transport approach to flow cytometry gating and population matching. BMC Bioinformatics, 21(1), pp. 479. doi:10.1186/s12859-020-03795-w (27 October 2020)
Groth EE, Weber M, Bahmer T, Pedersen F, Kirsten A, Börnigen D, Rabe KF, Watz H, Ammerpohl O, Goldmann T. Exploration of the sputum methylome and omics deconvolution by quadratic programming in molecular profiling of asthma and COPD: the road to sputum omics 2.0. Respir Res, 21(1), pp. 274. doi:10.1186/s12931-020-01544-4 (19 October 2020)
Lee DY, Kang Y, Im NR, Kim B, Kwon TK, Jung KY, Baek SK. Actin-Associated Gene Expression is Associated with Early Regional Metastasis of Tongue Cancer. Laryngoscope. doi:10.1002/lary.29025 (15 August 2020)
Li WH, Han JR, Ren PP, Xie Y, Jiang DY. Exploration of the mechanism of Zisheng Shenqi decoction against gout arthritis using network pharmacology. Comput Biol Chem, pp. 107358. doi:10.1016/j.compbiolchem.2020.107358 (8 August 2020)

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