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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 2022-07-05T05:30:07-04:00.

Cao Y, Dong Q, Wang D, Zhang P, Liu Y, Niu C. microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization. Bioinformatics. doi:10.1093/bioinformatics/btac438 (30 June 2022)

Metwally AA, Zhang T, Wu S, Kellogg R, Zhou W, Contrepois K, Tang H, Snyder M. Robust Identification of Temporal Biomarkers in Longitudinal Omics Studies. Bioinformatics. doi:10.1093/bioinformatics/btac403 (28 June 2022)

Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nat Commun, 13(1), pp. 3695. doi:10.1038/s41467-022-31411-3 (27 June 2022)

Arslan T, Pan Y, Mermelekas G, Vesterlund M, Orre LM, Lehtiö J. SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry. Nat Protoc. doi:10.1038/s41596-022-00699-2 (22 June 2022)

Persson S, Larsson C, Simonsson M, Ellström P. rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses. BMC Bioinformatics, 23(1), pp. 239. doi:10.1186/s12859-022-04781-0 (18 June 2022)

Han Y, Quan X, Chuang Y, Liang Q, Li Y, Yuan Z, Bian Y, Wei L, Wang J, Zhao Y. A multi-omics analysis for the prediction of neurocognitive disorders risk among the elderly in Macao. Clin Transl Med, 12(6), pp. e909. doi:10.1002/ctm2.909 (14 June 2022)

Movassagh M, Morton SU, Hehnly C, Smith J, Doan TT, Irizarry R, Broach JR, Schiff SJ, Bailey JA, Paulson JN. mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis. BMC Genomics, 23(1), pp. 439. doi:10.1186/s12864-022-08558-w (13 June 2022)

Pardo B, Spangler A, Weber LM, Page SC, Hicks SC, Jaffe AE, Martinowich K, Maynard KR, Collado-Torres L. spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data. BMC Genomics, 23(1), pp. 434. doi:10.1186/s12864-022-08601-w (10 June 2022)

Gangras P, Merchant A. surfaltr: An R/Bioconductor package to benchmark surface protein isoforms by rapid prediction and visualization of transmembrane topologies. Proteomics, pp. e2200002. doi:10.1002/pmic.202200002 (9 June 2022)

Wang ZB, Qu J, Xie P, Yang ZQ, Mao CX, Zhang Y, He ZW, Yang ZY, Mao XY, Liu ZQ. Integrative analysis of expression profile indicates the ECM receptor and LTP dysfunction in the glioma-related epilepsy. BMC Genomics, 23(1), pp. 430. doi:10.1186/s12864-022-08665-8 (8 June 2022)

Zhou L, Feng T, Xu S, Gao F, Lam TT, Wang Q, Wu T, Huang H, Zhan L, Li L, Guan Y, Dai Z, Yu G. ggmsa: a visual exploration tool for multiple sequence alignment and associated data. Brief Bioinform. doi:10.1093/bib/bbac222 (8 June 2022)

Song Y, Feng T, Cao W, Yu H, Zhang Z. Identification of Key Genes in Nasopharyngeal Carcinoma Based on Bioinformatics Analysis. Comput Intell Neurosci, 2022, pp. 9022700. doi:10.1155/2022/9022700 (7 June 2022)

Gu Z, Hübschmann D. Simplify enrichment: A bioconductor package for clustering and visualizing functional enrichment results. Genomics Proteomics Bioinformatics. doi:10.1016/j.gpb.2022.04.008 (6 June 2022)

Mallick H, Chatterjee S, Chowdhury S, Chatterjee S, Rahnavard A, Hicks SC. Differential expression of single-cell RNA-seq data using Tweedie models. Stat Med. doi:10.1002/sim.9430 (2 June 2022)

Pereira G, Guo Y, Silva E, Silva MF, Bevilacqua C, Charpigny G, Lopes-da-Costa L, Humblot P. Subclinical endometritis differentially affects the transcriptomic profiles of endometrial glandular, luminal, and stromal cells of postpartum dairy cows. J Dairy Sci, 105(7), pp. 6125-6143. doi:10.3168/jds.2022-21811 (28 May 2022)

Tian L, Li Z, Ma G, Zhang X, Tang Z, Wang S, Kang J, Liang D, Yu T. Metapone: a Bioconductor package for joint pathway testing for untargeted metabolomics data. Bioinformatics. doi:10.1093/bioinformatics/btac364 (27 May 2022)

Nan Q, Qinnan W, Chaoqun MA, Dexuan C, Haidong C, Yaoyao LU. Mechanism underlying efficacy of Shugan Sanjie decoction on plasma cell mastitis, based on network pharmacology and experimental verification. J Tradit Chin Med, 42(3), pp. 400-407. doi:10.19852/j.cnki.jtcm.20220311.004 (25 May 2022)

Rahmatbakhsh M, Moutaoufik MT, Gagarinova A, Babu M. HPiP: an R/Bioconductor package for predicting host-pathogen protein-protein interactions from protein sequences using ensemble machine learning approach. Bioinform Adv, 2(1), pp. vbac038. doi:10.1093/bioadv/vbac038 (23 May 2022)

Guan P, Cai W, Wu K, Jiang F, Wu J, Zhai X, Zeng M. Intercellular Communication-Related Molecular Subtypes and a Gene Signature Identified by the Single-Cell RNA Sequencing Combined with a Transcriptomic Analysis. Dis Markers, 2022, pp. 6837849. doi:10.1155/2022/6837849 (16 May 2022)

Wang KZ, Chaudhary Z, Qian J, Adanty C, Graff-Guerrero A, Gerretsen P, Zai CC, De Luca V. Differential Methylation Analysis of Suicidal Ideation Severity in Schizophrenia with the Illumina MethylationEPIC Array. Healthcare (Basel), 10(5). doi:10.3390/healthcare10050809 (27 April 2022)