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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 2021-06-22T23:00:07-04:00.

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)

Maksimovic J, Oshlack A, Phipson B. Gene set enrichment analysis for genome-wide DNA methylation data. Genome Biol, 22(1), pp. 173. doi:10.1186/s13059-021-02388-x (8 June 2021)

Xu S, Dai Z, Guo P, Fu X, Liu S, Zhou L, Tang W, Feng T, Chen M, Zhan L, Wu T, Hu E, Jiang Y, Bo X, Yu G. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Mol Biol Evol. doi:10.1093/molbev/msab166 (7 June 2021)

Zou Z, Hua K, Zhang X. HGC: fast hierarchical clustering for large-scale single-cell data. Bioinformatics. doi:10.1093/bioinformatics/btab420 (7 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)

Olgun G, Nabi A, Tastan O. NoRCE: non-coding RNA sets cis enrichment tool. BMC Bioinformatics, 22(1), pp. 294. doi:10.1186/s12859-021-04112-9 (2 June 2021)

Mo J, Zhang Z, Chen M, Mao H, Zhu Y, Li Y, Jiang H, Lin P, Chen X. [Construction of sepsis-associated competing endogenous RNA network based on Gene Expression Omnibus datasets and bioinformatic analysis]. Zhonghua Wei Zhong Bing Ji Jiu Yi Xue, 33(4), pp. 427-432. doi:10.3760/cma.j.cn121430-20210205-00211 (1 June 2021)

Ivanov M, Sandelin A, Marquardt S. TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes. BMC Bioinformatics, 22(1), pp. 290. doi:10.1186/s12859-021-04208-2 (31 May 2021)

Yu X, Kong DX. EnMCB: an R/bioconductor package for predicting disease progression based on methylation correlated blocks using ensemble models. Bioinformatics. doi:10.1093/bioinformatics/btab415 (29 May 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)

Lemoine GG, Scott-Boyer MP, Ambroise B, Périn O, Droit A. GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package. BMC Bioinformatics, 22(1), pp. 267. doi:10.1186/s12859-021-04179-4 (25 May 2021)

Mai Z, Li H, Chen G, Chen E, Liu L, Lun Z, Lai W, Zhou C, Yu S, Liu J, Chen S, Chen J, Liu Y. A Bioinformatics Investigation into the Pharmacological Mechanisms of Sodium-Glucose Co-transporter 2 Inhibitors in Diabetes Mellitus and Heart Failure Based on Network Pharmacology. Cardiovasc Drugs Ther. doi:10.1007/s10557-021-07186-y (24 May 2021)

Sun J, Zhao J, Yang Z, Zhou Z, Lu P. Identification of gene signatures and potential therapeutic targets for acquired chemotherapy resistance in gastric cancer patients. J Gastrointest Oncol, 12(2), pp. 407-422. doi:10.21037/jgo-21-81 (21 May 2021)

Liu M, Chen J, Wang X, Wang C, Zhang X, Xie Y, Zuo Z, Ren J, Zhao Q. MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations. Gigascience, 10(5). doi:10.1093/gigascience/giab036 (21 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)