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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.

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2020-03-30T20:20:06-04:00.

Chen L, Wu CT, Wang N, Herrington DM, Clarke R, Wang Y. debCAM: a Bioconductor R package for fully unsupervised deconvolution of complex tissues. Bioinformatics. doi:10.1093/bioinformatics/btaa205 (27 March 2020)

McLean C, Kujawinski EB. AutoTuner: High fidelity, robust, and rapid parameter selection for metabolomics data processing. Anal Chem. doi:10.1021/acs.analchem.9b04804 (26 March 2020)

Angerer P, Fischer DS, Theis FJ, Scialdone A, Marr C. Automatic identification of relevant genes from low-dimensional embeddings of single cell RNAseq data. Bioinformatics. doi:10.1093/bioinformatics/btaa198 (24 March 2020)

Zhu Y, Orre LM, Zhou Tran Y, Mermelekas G, Johansson HJ, Malyutina A, Anders S, Lehtiö J. DEqMS: a method for accurate variance estimation in differential protein expression analysis. Mol Cell Proteomics. doi:10.1074/mcp.TIR119.001646 (23 March 2020)

Mohamed A, Molendijk J, Hill MM. lipidr: A Software Tool for Data Mining and Analysis of Lipidomics Datasets. J Proteome Res. doi:10.1021/acs.jproteome.0c00082 (23 March 2020)

Itzel T, Neubauer M, Ebert M, Evert M, Teufel A. Hepamine - A Liver Disease Microarray Database, Visualization Platform and Data-Mining Resource. Sci Rep, 10(1), pp. 4760. doi:10.1038/s41598-020-61508-y (16 March 2020)

Tiberi S, Robinson MD. BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty. Genome Biol, 21(1), pp. 69. doi:10.1186/s13059-020-01967-8 (16 March 2020)

Boileau P, Hejazi NS, Dudoit S. Exploring High-Dimensional Biological Data with Sparse Contrastive Principal Component Analysis. Bioinformatics. doi:10.1093/bioinformatics/btaa176 (16 March 2020)

Li P, Xu Q, Hua X, Xie Z, Li J, Wang J. primirTSS: An R package for identifying cell-specific microRNA transcription start sites. Bioinformatics. doi:10.1093/bioinformatics/btaa173 (14 March 2020)

Yu G. Using ggtree to Visualize Data on Tree-Like Structures. Curr Protoc Bioinformatics, 69(1), pp. e96. doi:10.1002/cpbi.96 (13 March 2020)

Li Z, Guo Z, Cheng Y, Jin P, Wu H. Robust partial reference-free cell composition estimation from tissue expression. Bioinformatics. doi:10.1093/bioinformatics/btaa184 (13 March 2020)

Sharma G, Colantuoni C, Goff LA, Fertig EJ, Stein-O'Brien G. projectR: An R/Bioconductor package for transfer learning via PCA, NMF, correlation, and clustering. Bioinformatics. doi:10.1093/bioinformatics/btaa183 (13 March 2020)

Kitanovski S, Hoffmann D. IgGeneUsage: differential gene usage in immune repertoires. Bioinformatics. doi:10.1093/bioinformatics/btaa174 (12 March 2020)

Cresswell KG, Dozmorov MG. TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains. Front Genet, 11, pp. 158. doi:10.3389/fgene.2020.00158 (10 March 2020)

Lee C, Wang K, Qin T, Sartor MA. Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing. Front Genet, 11, pp. 199. doi:10.3389/fgene.2020.00199 (6 March 2020)

Nguyen T, Shafi A, Nguyen TM, Schissler AG, Draghici S. NBIA: a network-based integrative analysis framework - applied to pathway analysis. Sci Rep, 10(1), pp. 4188. doi:10.1038/s41598-020-60981-9 (6 March 2020)

Imkeller K, Ambrosi G, Boutros M, Huber W. gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection. Genome Biol, 21(1), pp. 53. doi:10.1186/s13059-020-1939-1 (2 March 2020)

Li L, Zuo X, Liu D, Luo H, Zhu H. The profiles of miRNAs and lncRNAs in peripheral blood neutrophils exosomes of diffuse cutaneous systemic sclerosis. J Dermatol Sci. doi:10.1016/j.jdermsci.2020.02.009 (28 February 2020)

Xu W, Tang M, Wang J, Wang L. Identification of the Active Constituents and Significant Pathways of Cangfu Daotan Decoction for the Treatment of PCOS Based on Network Pharmacology. Evid Based Complement Alternat Med, 2020, pp. 4086864. doi:10.1155/2020/4086864 (21 February 2020)

Williams J, Bravo HC, Tom J, Paulson JN. microbiomeDASim: Simulating longitudinal differential abundance for microbiome data. F1000Res, 8, pp. 1769. doi:10.12688/f1000research.20660.2 (17 October 2019)