R package for FLEX (Functional evaluation of experimental perturbations), a pipeline that utilizes several functional annotation resources (Complex, Pathway, GO BP) to establish reference standards for systematic evaluation of genome-wide CRISPR screens. FLEX can investigate both single mutant (fitness) or double mutant (genetic interaction) experiments. FLEX summarizes the functional signal captured by these experiments, both globally (gene-pair level) and locally (protein complex level, for example). FLEX highlights the functional information captured by an experiment (and/or scoring method) and also compare and contrast functional information from multiple experiments (or competing scoring schemes).
The associated manuscript is published in Moelcular systems biology and is available here. An overview of the FLEX pipeline is shown below:
FLEX_R is compatiable with R version >= 3.4.3 and doesn't have any dependency except for if someone wish to use the GIANT functional network as a standard ('org.Hs.eg.db' is needed in that case).
FLEX can be installed directly from github using install_github('csbio/FLEX_R') and this requires the 'devtools' package.
Please email to rahma118@umn.edu or mahfuz05062@gmail.com if you have any questions, comments, potential bugs or suggestions!