NOISeq is a tool for quality control of RNA-seq count data. The NOISeq can evaluate, among others, count distribution, per chromosome expression, and detected features. The NOISeqBIO module in the NOISeq package assesses false positives non-parametrically.
Sequencing; RNA-Seq; Gene expression
Tarazona S, Furio-Tari P, Turra D, Pietro AD, Nueda MJ, Ferrer A, Conesa A "Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package." Nucleic Acids Res. 2015 Dec 2;43(21):e140. 16. https://doi.org/10.1093/nar/gkv711
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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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