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'''Your friend to BRB-ArrayTools.'''
Shortcuts to some pages that may be useful to you!


== Features ==
{|
|style="width: 5%; border-width: 0px;"|[[File:Dna microarray45.png|link=Arraytools|BRB-ArrayTools]]||style="width: 20%; border-width: 0px;"|[[Arraytools|BRB-ArrayTools]]||style="width: 5%; border-width: 0px;"|[[File:linux48.png|link=Linux|Linux]]||style="width: 20%; border-width: 0px;"|[[Linux|Linux]]||style="width: 5%; border-width: 0px;"|[[File:R_logo48.png|link=R|R]]||style="width: 20%; border-width: 0px;"|[[R|R]]
|-
|| [[File:tai-chi48.png|link=Tai_Chi|Tai Chi]] || [[Tai_Chi|Tai Chi]] || [[File:heart48.png|link=Health|Health]] || [[Health|Health]] || [[File:raspberry48.png|link=Raspberry|Raspberry Pi]]  || [[Raspberry|Raspberry Pi]]
|-
|| [[File:docker48.png|link=Docker|Docker]]
|| [[Docker|Docker]]
|| [[File:recipe48.png|link=Recipes|Recipes]]
|| [[Recipes|Recipes]]
|| [[File:statistics48.png|link=Statistics|Statistics]]
|| [[Statistics|Statistics]]
|-
|| [[File:ubuntulogo48.png|link=Ubuntu|Ubuntu]]
|| [[Ubuntu|Ubuntu]]
|| [[File:vblogo48.png|link=Virtualbox|Virtualbox]]
|| [[Virtualbox|Virtualbox]]
|| [[File:beaglebone48.png|link=Beaglebone|Beaglebone]]
|| [[Beaglebone|Beaglebone]]
|}


=== Import from multiple data types ===
Expression data, Illumina methylation data, Copy number data (CGH-Tools), RNA-Seq count data processed through Galaxy web tool.
=== Sophisticated statistical analysis tools ===
Class comparison for differential expression, class prediction, graphical 2d and 3d interactive plots, gene set analysis, and more.


=== Comprehensive biological annotations ===
MC Li
Gene ontology, pathways, protein domain, broad msigdb, lymphoid signatures, experimentally verified transcription factor targets, computationally predicted microRNA targets.


== Screenshots ==
-----
 
==== [[File:BRB_HeatmapDendrogram.png|100px]] Heatmap and dendrogram generated from the BRCA sample dataset. ====
==== [[File:BRB_3Dplot.png|100px]] Interactive 3D scatterplot of samples from running the multidimensional scaling analysis on the Pomeroy dataset. ====
 
==== [[File:BRB_Scatterplot.png|100px]] Interactive 2D scatterplot of samples with gene annotation from a selected gene using right click menu. ====
 
==== [[File:VolcanoPlot.png|100px]] Interactive volcano plot from running a class comparison tool. ====
 
== FAQs  ==
 
=== How to install BRB-ArrayTools if you have 64-bit MS-Office? ===
There is no difference in terms of the installation.
 
=== If installation, I can not find the BRB-ArrayTools in Windows > Start > All Programs. ===
Check EXCEL.
 
=== Can I upgrade R? ===
Better not.
 
=== Can I install multiple versions of R? ===
Yes.
 
=== Rserve ===
 
Since version 4.3.0, BRB-ArrayTools started to use Rserve as a media for the communication between R and Excel. When Rserve is required, an R window will be pop up. This R window has a blue icon on the Windows' taskbar. If you accidentally close it, it will be automatically popped up when it is needed.
 
See my [[Rserve]] wiki page.
 
== Support ==
 
=== Send an email to [email protected] ===
 
Please provide enough information to us so we can understand the problem.
 
* If a bug report file was generated, be sure to send it to us.
* If the question is like 'what method or parameters should be choose to run my analysis', please consult other experienced people near you.
* Since the software depends on a couple factors like Windows operation system, MS-Office, R. Please provide us more detailed information about the software background including BRB-ArrayTools.
 
=== Check BRB-ArrayTools message board [http://linus.nci.nih.gov/cgi-bin/brb/board1.cgi] ===

Latest revision as of 20:51, 6 July 2022

Shortcuts to some pages that may be useful to you!

BRB-ArrayTools BRB-ArrayTools Linux Linux R R
Tai Chi Tai Chi Health Health Raspberry Pi Raspberry Pi
Docker Docker Recipes Recipes Statistics Statistics
Ubuntu Ubuntu Virtualbox Virtualbox Beaglebone Beaglebone


MC Li