README.md

In mummlab/ARQiv: : ARQiv-HTS,Preparing for and Completing Whole-Organism Screening at High-througput rates

ARQiv

ARQiv is a R package for Preparing for and Completing Whole-Organism Screening at High-througput rates.

Overview

The ARQiv R* package includes functions that fall into two categories - those applied to 'Pre-screening Assay Optimization' and 'Compound Analysis'. The functions allow the user to calculate background signal, determine sample size, run quality control tests, perform virtual experiments to simulate compound efficacy - and finally, to perform compound analysis during iterative drug screen cycles.

The ARQiv package is a part of the published paperpaper name.

Package Installation

• STEP 1: Install the latest version of R(for Windows (https://cran.r-project.org/bin/windows/base/) or Mac(https://cran.r-project.org/bin/macosx/)) and RStudio(https://www.rstudio.com/products/rstudio/download2/) on your computer.
• STEP 2: To install ARQiv package via Github, the user must have installed devtools by running the following commands in RStudio Console window:

install.packages("devtools")
library(devtools)

• STEP 3: To use the graphical user interface (GUI) in ARQiv package, the user must have first installed RGtk2, GTK2+ with commands in RStudio Console.

STEP 3a: for Windows

install.packages("RGtk2",depen=T)
library(RGtk2)

There will be a notice for missing GTK. Choose "Install GTK+" when prompted - this will take ~1 minute to complete. Afterwards the user needs to restart R/Rstudio.

STEP 3b: for Mac

Install GTK 2.24. And use command

install.packages("RGtk2",depen=T)

in RStudio console window. Then user need to restart R/Rstudio.

• STEP 4: Complete RGtk2,gWidgets2RGtk2 packages installation by commands in RStudio console window:

library(RGtk2)
install.packages("gWidgets2RGtk2")
library(gWidgets2RGtk2)

• STEP 5: Install ARQiv package and open GUI window with the following command in RStudio console window:

devtools::install_github("mummlab/ARQiv")
library(ARQiv)
GUI()

Further questions

Author: David T. White, Arife Unal Eroglu, Guohua Wang,Liyun Zhang,Sumitra Sengupta,Ding Ding,Surendra Rajpurohit,Steven L. Walker,Hongkai Ji,Jiang Qian,Jeff S. Mumm

Any questions about the package, please contact Maintainer: David T. White [e-mail], Ding Ding [e-mail] or open an issue at Github.

mummlab/ARQiv documentation built on May 23, 2019, 8:22 a.m.