genArise: Microarray Analysis tool

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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.

Author
Ana Patricia Gomez Mayen <pgomez@ifc.unam.mx>,\\ Gustavo Corral Guille <gcorral@ifc.unam.mx>, \\ Lina Riego Ruiz <lriego@ifc.unam.mx>,\\ Gerardo Coello Coutino <gcoello@ifc.unam.mx>
Date of publication
None
Maintainer
IFC Development Team <info-genarise@ifc.unam.mx>
License
file LICENSE
Version
1.50.0
URLs

View on Bioconductor

Man pages

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

Files in this package

genArise/DESCRIPTION
genArise/LICENSE
genArise/NAMESPACE
genArise/R
genArise/R/Zscore.R
genArise/R/applications.R
genArise/R/base.R
genArise/R/baseGUI.R
genArise/R/classes.R
genArise/R/genArise.R
genArise/R/genMerge.R
genArise/R/help.R
genArise/R/imageLimma.R
genArise/R/input.R
genArise/R/openProyect.R
genArise/R/openswap.R
genArise/R/operations.R
genArise/R/output.R
genArise/R/plot.R
genArise/R/postAnalysis.R
genArise/R/swap.R
genArise/R/var.R
genArise/build
genArise/build/vignette.rds
genArise/data
genArise/data/Simon.rda
genArise/data/WT.dataset.rda
genArise/inst
genArise/inst/doc
genArise/inst/doc/genArise.R
genArise/inst/doc/genArise.Rnw
genArise/inst/doc/genArise.pdf
genArise/man
genArise/man/DataSet-class.Rd
genArise/man/Simon.Rd
genArise/man/Spot-class.Rd
genArise/man/WT.dataset.Rd
genArise/man/Zscore.Rd
genArise/man/Zscore.plot.Rd
genArise/man/Zscore.points.Rd
genArise/man/a.arise.Rd
genArise/man/alter.unique.Rd
genArise/man/analysis.window.Rd
genArise/man/annotations.Rd
genArise/man/back.gui.Rd
genArise/man/bg.correct.Rd
genArise/man/classes.Rd
genArise/man/create.project.Rd
genArise/man/cys.plot.Rd
genArise/man/filter.spot.Rd
genArise/man/genArise.Rd
genArise/man/genArise.init.Rd
genArise/man/genMerge.Rd
genArise/man/get.Zscore.Rd
genArise/man/get.values.Rd
genArise/man/global.norm.Rd
genArise/man/graphic.choose.Rd
genArise/man/grid.norm.Rd
genArise/man/help.Rd
genArise/man/i.arise.Rd
genArise/man/imageLimma.Rd
genArise/man/m.arise.Rd
genArise/man/ma.plot.Rd
genArise/man/make.swap.Rd
genArise/man/meanUnique.Rd
genArise/man/note.Rd
genArise/man/old.project.Rd
genArise/man/post.analysis.Rd
genArise/man/principal.Rd
genArise/man/projects.select.Rd
genArise/man/r.arise.Rd
genArise/man/read.dataset.Rd
genArise/man/read.spot.Rd
genArise/man/reset.history.Rd
genArise/man/ri.plot.Rd
genArise/man/set.grid.properties.Rd
genArise/man/set.history.project.Rd
genArise/man/set.path.project.Rd
genArise/man/set.project.properties.Rd
genArise/man/single.norm.Rd
genArise/man/spotUnique.Rd
genArise/man/swap.select.Rd
genArise/man/trim.Rd
genArise/man/write.dataSet.Rd
genArise/man/write.spot.Rd
genArise/man/write.zscore.Rd
genArise/vignettes
genArise/vignettes/genArise.Rnw
genArise/vignettes/help
genArise/vignettes/help/contents
genArise/vignettes/icons
genArise/vignettes/icons/acroread.png
genArise/vignettes/icons/analysis.png
genArise/vignettes/icons/cy3vscy5.png
genArise/vignettes/icons/editor.png
genArise/vignettes/icons/filter.png
genArise/vignettes/icons/help.png
genArise/vignettes/icons/logout.png
genArise/vignettes/icons/norm.png
genArise/vignettes/icons/regresar.png
genArise/vignettes/icons/swap.png
genArise/vignettes/icons/zscore.png