shiny app by the Gehan Lab to graph JTK Cycle Output (Hughes et al. 2010)
This repository is associated with DOI:XXXXX please cite:
Huang H., Gehan M.A., Huss S., Alvarez S., Lizarraga C., Gruebbling E., Naldrett M., Bindbeutel R., Evans B., Mockler T.C., Nusinow D.A. Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots. XXXXXXX.(2017). DOI
Raw data and processed data can be found on NCBI’s Gene Expression Omnibus (GEO; Edgar et al.2002, Barrett et al. 2013 ) and are accessible with identification number GSE97739 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97739). If code or data is used from this repository please cite the paper above.
The app associated with this repository can be found at: http://shiny.danforthcenter.org/diel-explorer/
Citations: Hughes, M.E., Hogenesch, J.B., and Kornacker, K. (2010). JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J. Biol. Rhythms 25, 372–380.
Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res. 2002 Jan 1;30(1):207-10
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5.