XBSeq is an R tool for genome-wide expression analysis of RNA-seq data. The XBSeq algorithm uses a statistical approach in which observed signals are a convolution of real expression signals and sequencing noises. It assumes the reads that map on intergenic regions are distributed according to Poisson and distinguishes signals using the negative binomial distribution.
Gene expression; RNA-Seq
Chen HI, Liu Y, Zou Y, Lai Z, Sarkar D, Huang Y, Chen Y "Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads." BMC Genomics. 2015;16 Suppl 7:S14. Jun 11. https://doi.org/10.1186/1471-2164-16-S7-S14
PMID: 26099631
PMCID: PMC4474535
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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