README.md

In mummlab/Arqiv2:

Arqiv2

Arqiv2 is a R package for Real-Time Data Analysis of Compounds Performance Relative to Controls in Primary Screening.

Overview

The Arqiv2 package allows the user to plot signal to background ratios, strictly standardized mean difference (SSMD) scores, microplate heat map and generate SSMD score table of each compound.

The Arqiv2 package is a part of the paper "Large-scale Phenotypic Drug Screen Identifies Neuroprotectants in Zebrafish and Mouse Models of Retinitis Pigmentosa".

Package Installation

• STEP 1: Install the latest version of R(for Windows (https://cran.r-project.org/bin/windows/base/) and RStudio(https://www.rstudio.com/products/rstudio/download2/) on your computer. R version 3.6.3 is prefered.
• STEP 2: To install Arqiv2 package via Github, the user must have installed Rtools and devtools by running the following commands in RStudio Console window:

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

• STEP 3: To use the graphical user interface (GUI) in Arqiv2 package, the user must have first installed RGtk2, GTK2+ with commands in RStudio Console.

only for Windows

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

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

* STEP 4: Complete RGtk2,gWidgets2RGtk2 packages installation by commands in RStudio console window:
```{r}
library(RGtk2)
install.packages("gWidgets2RGtk2")
library(gWidgets2RGtk2)

• STEP 5: Install Arqiv2 package and open GUI window with the following command in RStudio console window:

devtools::install_github("mummlab/Arqiv2")
library(Arqiv2)
GUI()

Further questions

Author: Liyun Zhang, Ding Ding

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

mummlab/Arqiv2 documentation built on Dec. 21, 2021, 11:01 p.m.