Package: genArise 1.89.0

IFC Development Team

genArise: Microarray Analysis tool

genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.

Authors:Ana Patricia Gomez Mayen <[email protected]>,\\ Gustavo Corral Guille <[email protected]>, \\ Lina Riego Ruiz <[email protected]>,\\ Gerardo Coello Coutino <[email protected]>

genArise_1.89.0.tar.gz
genArise_1.89.0.zip(r-4.7)genArise_1.89.0.zip(r-4.6)genArise_1.89.0.zip(r-4.5)
genArise_1.89.0.tgz(r-4.6-any)genArise_1.89.0.tgz(r-4.5-any)
genArise_1.89.0.tar.gz(r-4.7-any)genArise_1.89.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
genArise/json (API)

# Install 'genArise' in R:

install.packages('genArise', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

Simon - Dataset: Little fragment of a microarray from IFC UNAM
WT.dataset - Microarray from the IFC

On BioConductor:genArise-1.89.0(bioc 3.24)genArise-1.88.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray twochannel preprocessing

4.30 score 2 scripts 16 mentions 48 exports 4 dependencies

Last updated from:fcaf847e16. Checks:1 ERROR, 7 WARNING, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	153
linux-devel-x86_64	WARNING	145
source / vignettes	OK	194
linux-release-x86_64	WARNING	205
macos-release-arm64	WARNING	97
macos-oldrel-arm64	WARNING	81
windows-devel	WARNING	79
windows-release	WARNING	125
windows-oldrel	WARNING	74
wasm-release	FAIL	100

Exports:a.arise alter.unique analysis.window annotations back.gui bg.correct create.project cys.plot filter.spot genArise genArise.init genMerge get.values get.Zscore global.norm graphic.choose grid.norm help i.arise imageLimma m.arise ma.plot make.swap meanUnique note old.project post.analysis principal projects.select r.arise read.dataset read.spot reset.history ri.plot set.grid.properties set.history.project set.path.project set.project.properties single.norm spotUnique swap.select trim write.dataSet write.spot write.zscore Zscore Zscore.plot Zscore.points

Dependencies:lattice locfit tkrplot xtable

genAriseGUI Vignette

Introduction | The genArise Package's Functions | The genArise GUI

Rendered fromgenArise.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A Arise	a.arise
Remove Duplicates	alter.unique
Analysis.window	analysis.window
Gene Annotations	annotations
Return to the last window	back.gui
Background Correction	bg.correct
Classes Defined by this Package	classes
Create directorie for the project and its results and graphics	create.project
Data Visualization: log2(Cy3) vs log2(Cy5)	cys.plot
DataSet - class	DataSet-class
Intensity-based filtering of array elements	filter.spot
GUI: Graphical User Interface	genArise
genArise.init	genArise.init
genMerge: Post-Genomic Analysis	genMerge
Auxiliar function for post-analysis	get.values
Swap from Files	get.Zscore
Global Normalization of Spot	global.norm
Graphic choose	graphic.choose
Normalization by grid of Spot	grid.norm
Help of genArise	help
I Arise	i.arise
Image Plot of Microarray	imageLimma
M Arise	m.arise
Data Visualization: M vs. A plot	ma.plot
Swap analysis	make.swap
Remove Duplicates	meanUnique
note	note
Open previous project	old.project
Set-combinatorial analysis	post.analysis
Principal window of genAriseGUI	principal
File selector	projects.select
Get R value	r.arise
Read Dataset from File	read.dataset
Read Spot from File	read.spot
Reset the prj history file	reset.history
Data Visualization: R vs I	ri.plot
set.grid.properties	set.grid.properties
Save the history of a project	set.history.project
set.path.project	set.path.project
set.project.properties	set.project.properties
Dataset: Little fragment of a microarray from IFC UNAM	Simon
Swap from Files	single.norm
Spot - class	Spot-class
Replicate filtering	spotUnique
Dye swap files selector	swap.select
Trim	trim
Write dataSet	write.dataSet
Write Spot	write.spot
Write Z-score data	write.zscore
Microarray from the IFC	WT.dataset
Z-scores for identifying differential expression	Zscore
Z-score Data Visualization: R vs I or M vs A	Zscore.plot
Z-score Window	Zscore.points