statTarget2

A streamlined tool provides graphical user interface for quality control based signal correction (QC-RFSC, QC-RLSC, Combat), integration of metabolomics and proteomics data from multi-batch experiments, and the comprehensive statistic analysis. (URL: https://stattarget.github.io)

For details and latest version see https://stattarget.github.io/docs/

Package vignettes: Vignettes

Reference manual: Manual

Demo data: Data

Example reports: Reports

Binary Package: statTarget2_WindowsOnly.zip

Citation

Please cite the following article when using statTarget or QC-RFSC algorithm:

Luan H., Ji F., Chen Y., Cai Z. (2018) statTarget: A streamlined tool for signal drift correction and interpretations of quantitative mass spectrometry-based omics data. Analytica Chimica Acta. dio: https://doi.org/10.1016/j.aca.2018.08.002

Luan H., Ji F., Chen Y., Cai Z. (2018) Quality control-based signal drift correction and interpretations of metabolomics/proteomics data using random forest regression. bioRxiv 253583; doi: https://doi.org/10.1101/253583

System requirements

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Dependent on R

If you did not install the R software yet,you can download R >= 3.6.0 from https://www.r-project.org

Installation

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Install “statTarget2” at the Bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

BiocManager::install("statTarget", version = "devel") 

library(statTarget)
statTargetGUI()

Install “statTarget2” at the Github

if (!requireNamespace("devtools", quietly = TRUE))

install.packages("devtools")

devtools::install_github("statTarget/statTarget2")

library(statTarget)

statTargetGUI()

IMPORTANCE: for mac PC, XQuartz instead of X11 support should be installed for the Graphical User Interface (GUI). Download it from https://www.xquartz.org.

RGTK2 is a binding for R to the GTK2 library and dependent libraries, and a multi-platform package for creating graphical user interfaces. If you have any problems about RGTK2 installation, see the related installation information for R and GTK on Windows/Mac OS at https://gist.github.com/sebkopf/9405675.

We recommend the R 3.6.0 and RGtk2 for mac OS paltform. The R 3.6.0 and RGtk2 sailed through the test. If you have multiple versions of R framework installed, RSwitch - a small GUI that allows you to switch between R versions quickly. Download it from https://r.research.att.com