ImpulseDE is an R tool for differentially expressed genes (DEGs) in RNA-seq and scRNA-seq time-course data. The ImpulseDE can report DEGs across time points over time in datasets with single or multiple conditions. It includes quality values for DEGs, impulse model parameters, fitted values for genes, and can use multi-threading.
Gene expression; Sequencing; Transcriptomics
Sander J, Schultze JL, Yosef N "ImpulseDE: detection of differentially expressed genes in time series data using impulse models." Bioinformatics. 2017 Mar 1;33(5):757-759. https://doi.org/10.1093/bioinformatics/btw665
PMID: 27797772
PMCID: PMC5859984
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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