R/Transcriptomic_Profile.R

In isarnassiri/CMEA: CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile

#'@title{Transcriptomic Profiles of U-2 OS cells in response to the perturbations with drugs and small molecules}
#'@description{
#'We demonstrate the application of the CMEA package by using the transcriptomic and single cell morphological profiles of human bone osteosarcoma cells (U-2 OS cells)
#'in response to the 9515 drugs or small molecule compounds (1). The raw data include the transcripotimic profiles of 20340 drugs and small compound moleculess, 
#'and processed version of this data is available as supplementary of (2). The intersection of transcriptomic and single-cell morphological profiles includes 9515 
#'drugs and small compound molecules, and use as a backend repository of CMEA package. The transcriptomic profile in backend repository is 9515*978 matric, 
#'including the fold change of the 978 landmark gene expression in response to the treatment of U-2 OS cells with 9515 drugs and small compound molecules.
#'We use subset of complete data set as an example (162 profles), and complete data are available at (https://bitbucket.org/isarnassiri/cmeadata).
#'}
#'@references{
#'1. Wawer, M.J., Jaramillo, D.E., Dancik, V., Fass, D.M., Haggarty, S.J., Shamji, A.F., Wagner, B.K., Schreiber, S.L. and Clemons, P.A. (2014) Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles. Journal of Biomolecular Screening, 19,738-748.
#'2. Wang, Z., Clark, N.R. and Ma'ayan, A. (2016) Drug-induced adverse events prediction with the LINCS L1000 data. Bioinformatics, 32, 2338-2345.
#'}
"Transcriptomic_Profile"