derfinder is a tool for differential expression analysis of RNA-seq data. The derfinder package provides single base-level F-statistics and identification at differentially expressed region (DER) levels. The derfinder algorithm uses a bump-hunting method for the identification of differentially expressed regions and among others, multi-group and time-course analyses. The derfinder package also contains visualization functions.
RNA-Seq
Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE "Flexible expressed region analysis for RNA-seq with derfinder." Nucleic Acids Res. 2017 Jan 25;45(2):e9. 29. https://doi.org/10.1093/nar/gkw852
PMID: 27694310
PMCID: PMC5314792
Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT "Differential expression analysis of RNA-seq data at single-base resolution" Biostatistics. 2014 Jul;15(3):413-26. https://doi.org/10.1093/biostatistics/kxt053
PMID: 24398039
PMCID: PMC4059460
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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