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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("genArise")
AuthorAna 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>
Bioconductor views Microarray Preprocessing TwoChannel
Date of publicationNone
MaintainerIFC Development Team <info-genarise@ifc.unam.mx>
Licensefile LICENSE
Version1.52.0
http://www.ifc.unam.mx/genarise

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

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.