Package: genArise 1.83.0

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]>

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genArise.pdf |genArise.html✨
genArise/json (API)

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

Peer review:

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

On BioConductor:genArise-1.81.0(bioc 3.20)genArise-1.80.0(bioc 3.19)

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

microarraytwochannelpreprocessing

4.30 score 1 scripts 223 downloads 16 mentions 48 exports 4 dependencies

Last updated 23 days agofrom:26bc1fdb1e. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 30 2024
R-4.4-macWARNINGOct 30 2024
R-4.3-winWARNINGOct 30 2024
R-4.3-macWARNINGOct 30 2024

Exports:a.arisealter.uniqueanalysis.windowannotationsback.guibg.correctcreate.projectcys.plotfilter.spotgenArisegenArise.initgenMergeget.valuesget.Zscoreglobal.normgraphic.choosegrid.normhelpi.ariseimageLimmam.arisema.plotmake.swapmeanUniquenoteold.projectpost.analysisprincipalprojects.selectr.ariseread.datasetread.spotreset.historyri.plotset.grid.propertiesset.history.projectset.path.projectset.project.propertiessingle.normspotUniqueswap.selecttrimwrite.dataSetwrite.spotwrite.zscoreZscoreZscore.plotZscore.points

Dependencies:latticelocfittkrplotxtable

genAriseGUI Vignette

Rendered fromgenArise.Rnwusingutils::Sweaveon Oct 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
A Arisea.arise
Remove Duplicatesalter.unique
Analysis.windowanalysis.window
Gene Annotationsannotations
Return to the last windowback.gui
Background Correctionbg.correct
Classes Defined by this Packageclasses
Create directorie for the project and its results and graphicscreate.project
Data Visualization: log2(Cy3) vs log2(Cy5)cys.plot
DataSet - classDataSet-class
Intensity-based filtering of array elementsfilter.spot
GUI: Graphical User InterfacegenArise
genArise.initgenArise.init
genMerge: Post-Genomic AnalysisgenMerge
Auxiliar function for post-analysisget.values
Swap from Filesget.Zscore
Global Normalization of Spotglobal.norm
Graphic choosegraphic.choose
Normalization by grid of Spotgrid.norm
Help of genArisehelp
I Arisei.arise
Image Plot of MicroarrayimageLimma
M Arisem.arise
Data Visualization: M vs. A plotma.plot
Swap analysismake.swap
Remove DuplicatesmeanUnique
notenote
Open previous projectold.project
Set-combinatorial analysispost.analysis
Principal window of genAriseGUIprincipal
File selectorprojects.select
Get R valuer.arise
Read Dataset from Fileread.dataset
Read Spot from Fileread.spot
Reset the prj history filereset.history
Data Visualization: R vs Iri.plot
set.grid.propertiesset.grid.properties
Save the history of a projectset.history.project
set.path.projectset.path.project
set.project.propertiesset.project.properties
Dataset: Little fragment of a microarray from IFC UNAMSimon
Swap from Filessingle.norm
Spot - classSpot-class
Replicate filteringspotUnique
Dye swap files selectorswap.select
Trimtrim
Write dataSetwrite.dataSet
Write Spotwrite.spot
Write Z-score datawrite.zscore
Microarray from the IFCWT.dataset
Z-scores for identifying differential expressionZscore
Z-score Data Visualization: R vs I or M vs AZscore.plot
Z-score WindowZscore.points