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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 2021-07-26T12:00:08-04:00.

Béné MC, Lacombe F, Porwit A. Unsupervised flow cytometry analysis in hematological malignancies: A new paradigm. Int J Lab Hematol, 43 Suppl 1, pp. 54-64. doi:10.1111/ijlh.13548 (22 July 2021)
Dursun C, Kwitek A, Bozdag S. PhenoGeneRanker: Gene and Phenotype Prioritization Using Multiplex Heterogeneous Networks. IEEE/ACM Trans Comput Biol Bioinform, PP. doi:10.1109/TCBB.2021.3098278 (20 July 2021)
Chen W, Lin T, He Q, Yang P, Zhang G, Huang F, Wang Z, Peng H, Li B, Liang D, Wang H. Study on the potential active components and molecular mechanism of Xiao Huoluo Pills in the treatment of cartilage degeneration of knee osteoarthritis based on bioinformatics analysis and molecular docking technology. J Orthop Surg Res, 16(1), pp. 460. doi:10.1186/s13018-021-02552-w (17 July 2021)
Fischer S, Crow M, Harris BD, Gillis J. Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor. Nat Protoc. doi:10.1038/s41596-021-00575-5 (7 July 2021)
Castellano-Escuder P, González-Domínguez R, Carmona-Pontaque F, Andrés-Lacueva C, Sánchez-Pla A. POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis. PLoS Comput Biol, 17(7), pp. e1009148. doi:10.1371/journal.pcbi.1009148 (1 July 2021)
Voisin S, Jacques M, Landen S, Harvey NR, Haupt LM, Griffiths LR, Gancheva S, Ouni M, Jähnert M, Ashton KJ, Coffey VG, Thompson JM, Doering TM, Gabory A, Junien C, Caiazzo R, Verkindt H, Raverdy V, Pattou F, Froguel P, Craig JM, Blocquiaux S, Thomis M, Sharples AP, Schürmann A, Roden M, Horvath S, Eynon N. Meta-analysis of genome-wide DNA methylation and integrative omics of age in human skeletal muscle. J Cachexia Sarcopenia Muscle. doi:10.1002/jcsm.12741 (30 June 2021)
Wang Y, Hannon E, Grant OA, Gorrie-Stone TJ, Kumari M, Mill J, Zhai X, McDonald-Maier KD, Schalkwyk LC. DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy. BMC Genomics, 22(1), pp. 484. doi:10.1186/s12864-021-07675-2 (28 June 2021)
Zhou Y, Yang B, Wang J, Zhu J, Tian G. A scaling-free minimum enclosing ball method to detect differentially expressed genes for RNA-seq data. BMC Genomics, 22(1), pp. 479. doi:10.1186/s12864-021-07790-0 (26 June 2021)
Dixit G, Zheng Y, Parker B, Wen J. Identification of Alternative Splicing and Polyadenylation in RNA-seq Data. J Vis Exp(172). doi:10.3791/62636 (24 June 2021)
Blumenberg L, Kawaler EA, Cornwell M, Smith S, Ruggles KV, Fenyö D. BlackSheep: A Bioconductor and Bioconda Package for Differential Extreme Value Analysis. J Proteome Res, 20(7), pp. 3767-3773. doi:10.1021/acs.jproteome.1c00190 (24 June 2021)
Tjeldnes H, Labun K, Torres Cleuren Y, Chyżyńska K, Świrski M, Valen E. ORFik: a comprehensive R toolkit for the analysis of translation. BMC Bioinformatics, 22(1), pp. 336. doi:10.1186/s12859-021-04254-w (19 June 2021)
Wolfer AM, Correia GDS, Sands CJ, Camuzeaux S, Yuen AHY, Chekmeneva E, Takáts Z, Pearce JTM, Lewis MR. peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in LC-MS profiling datasets. Bioinformatics. doi:10.1093/bioinformatics/btab433 (14 June 2021)
Knight P, Gauthier ML, Pardo CE, Darst RP, Kapadia K, Browder H, Morton E, Riva A, Kladde MP, Bacher R. Methylscaper: an R/shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data. Bioinformatics. doi:10.1093/bioinformatics/btab438 (14 June 2021)
Kato H, Shimizu M, Urano T. Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos. BMC Bioinformatics, 22(1), pp. 322. doi:10.1186/s12859-021-04240-2 (13 June 2021)
Chen L, Zheng J, Yang Z, Chen W, Wang Y, Wei P. Identification of key candidate genes in local dorsal root ganglion inflammation by integrated bioinformatics analysis. Exp Ther Med, 22(2), pp. 821. doi:10.3892/etm.2021.10253 (2 June 2021)
Wang L, He T, Liu J, Tai J, Wang B, Zhang L, Quan Z. Revealing the Immune Infiltration Landscape and Identifying Diagnostic Biomarkers for Lumbar Disc Herniation. Front Immunol, 12, pp. 666355. doi:10.3389/fimmu.2021.666355 (27 May 2021)
Sun F, Zhou JL, Peng PJ, Qiu C, Cao JR, Peng H. Identification of Disease-Specific Hub Biomarkers and Immune Infiltration in Osteoarthritis and Rheumatoid Arthritis Synovial Tissues by Bioinformatics Analysis. Dis Markers, 2021, pp. 9911184. doi:10.1155/2021/9911184 (17 May 2021)
Rian K, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Esteban-Medina M, Alamo-Alvarez I, Peña-Chilet M, Dopazo J. Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. Comput Struct Biotechnol J, 19, pp. 2968-2978. doi:10.1016/j.csbj.2021.05.022 (15 May 2021)
Rodríguez TC, Dadafarin S, Pratt HE, Liu P, Amrani N, Zhu LJ. Genome-wide detection and analysis of CRISPR-Cas off-targets. Prog Mol Biol Transl Sci, 181, pp. 31-43. doi:10.1016/bs.pmbts.2021.01.012 (4 March 2021)
Wagner J, Kancherla J, Braccia D, Matsumara J, Felix V, Crabtree J, Mahurkar A, Corrada Bravo H. Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz. F1000Res, 9, pp. 601. doi:10.12688/f1000research.24345.2 (12 June 2020)

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