An R package for interactive analysis of RNA -seq data, specifically lncRNA, mRNA, related to ceRNA regulatory networks in cancer data sets from the Genomic Data Commons (GDC). GDCRNATools also has functions for downloading and organizing the GDC data.
Functional, regulatory and non-coding RNA; RNA; Data management; RNA-seq; Gene expression; Gene regulation
Li R, Qu H, Wang S, Wei J, Zhang L, Ma R, Lu J, Zhu J, Zhong WD, Jia Z "GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC." Bioinformatics. 2018 Jul 15;34(14):2515-2517. https://doi.org/10.1093/bioinformatics/bty124
PMID: 29509844
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600
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