Download Shareware and Freeware Software for Windows, Linux, Macintosh, PDA

line Home  |  About Us  |  Link To Us  |  FAQ  |  Contact

Serving Software Downloads in 976 Categories, Downloaded 29.984.484 Times

ErmineJ 2.1.21

Company: Paul Pavlidis
Date Added: July 09, 2013  |  Visits: 209

ErmineJ

Report Broken Link
Printer Friendly Version


Product Homepage
Download (16 downloads)

ErmineJ performs analyses of gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ.<br /><br />A description of ermineJ was published as: Lee H.K., Braynen W., Keshav K. and Pavlidis P. (2005) ErmineJ: Tool for functional analysis of gene expression data sets. BMC Bioinformatics 6:269. (Download a PDF or view the abstract).<br /><br />While ErmineJ has a full user's manual, there is a Nature Protocols paper that contains many additional tips and a detailed walk-through.<br /><br />ErmineJ can be downloaded here , or run ErmineJ right now using WebStart if you already have Java installed.<br /><br />Major features include:<br /><br /> * Implementation of multiple methods for gene set analysis:<br /> o Over-representation analysis<br /> o A resampling-based method that uses gene scores<br /> o A rank-based method that uses gene scores<br /> o A resampling-based method that uses correlation between gene expression profiles (a type of "cluster-enrichment" analysis).<br /> * Gene sets receive statistical scores (p-values), and multiple test correction is supported.<br /> * Support of the Gene Ontology terminology; users can choose which aspects to analyze.<br /> * User files use simple text formats.<br /> * Users can modify gene sets or create new ones.<br /> * The results can be visualized within the software.<br /> * It is simple to compare multiple analyses of the same data set with different settings.<br /> * User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results.<br /> * For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code

Requirements: No special requirements
Platforms: Mac, Mac OSX
Keyword: Analyses Analysis Application Correction Erminej Expression Interface Method Multiple Ontology Pvalues Resamplingbased Results Scores Simple Software Statistical Users
Users rating: 0/10

License: Freeware Size: 21.13 MB
ERMINEJ RELATED
Utilities  -  TraffStats 0.9.1
TraffStats is a monitoring and traffic analysis application that uses SNMP to collect data from any enabled device. It has the ability to generate graphs (using jpgraph) with the option to compare and sum up different devices. The project has a...
112.64 KB  
Utilities  -  TH-03 1.0.0
TH-03 is an application that provides an interface to the Picotech TH-03 digital thermometer. The project generates logfiles on demand and can run as a daemon. Building and installing Type: ./configure && make Then you should have an...
133.12 KB  
Modules  -  Woopra Analytics Plugin 1.4.0.3
Woopra is the a comprehensive, information rich, easy to use, real-time Web tracking and analysis application. An Woopra account is needed for this plugin to work. InstallationUnpack and upload it to the /wp-content/plugins/ directory.Activate the...
 
Audio Tools  -  AudioCarver for Linux 0.5.1.1
AudioCarver is a music composition application featuring a user interface based on 3d modeling. Examples of its audio and visual output can be found at audiosculptures.com.
614.4 KB  
Version Control Tools  -  SVNAccess 1.0.4
SVNAccess is a small Web application which lets one manage the access to SVN repositories through a simple interface. SVNAccess uses existing Apache password files/users and stores information in a MySQL database in order to generate an...
10.24 KB  
Multimedia & Graphics  -  SilacRatioAnalyser 1.2
SilacRatioAnalyser is specially designed as a simple, accessible and easy-to-use ratio analysis application. SilacRatioAnalyser was developed with the help of the Java programming language and can run on multiple platforms.
 
Remote Computing Tools  -  Proxy Log Storage Enterprise Edition 2.21 Buid 0105
Proxy Log Storage Enterprise Edition is the fastest and most powerful analysis application for monitoring the efficiency corporate Internet usage of your Proxy server. Log Explorer creates dynamic reports on-the-fly. Also, you can easily get...
 
Specialized Tools  -  Little Install Builder 1.0 Build 005
Little Install Builder is a simple SDI application with a tabbed interface where you can enter all the information needed by the setup program. For example: assign shortcuts and other setup specific variables, add files. You can also use the...
 
Sports  -  RallyAnalytics 2.0
RallyAnalytics is a unique analytical platform that helps the hobby rally racer perform like a professional but on an amateur's budget. This easy-to-use mobile application functions as an interface between your car and our web-based...
1024 KB  
Specialized Tools  -  inPreso Screens 1.0
inPreso Screens is a simple software mock-ups and website wireframes design application. With inPreso Screens you can design low and high-fidelity wireframes, add simple interactivity and instantly publish your wireframes on web. Visual task...
2.61 MB  
NEW DOWNLOADS IN MACINTOSH SOFTWARE, EDUCATION
Macintosh Software  -  MacX Free DVD to MP4 Converter for Mac 4.2.3
MacX Free DVD to MP4 Converter for Mac is an innovative yet free DVD to MP4 ripper software for Mac users without any functional limitation or watermark. It is able to convert DVDs including copy protected DVD movies to MP4, FLV, MP3 music on Mac...
36.23 MB  
Macintosh Software  -  MacX Free Rip DVD to QuickTime for Mac 4.1.9
MacX Free Rip DVD to QuickTime for Mac is totally free yet versatile DVD to QuickTime ripper software for Mac users to free rip both normal and copy-protected DVDs to QuickTime MOV, MP4 on Mac with excellent image quality. Besides the powerful...
36.3 MB  
Macintosh Software  -  MacX QuickTime Video Converter Free 4.1.9
MacX QuickTime Video Converter Free Edition is the best program designed for Mac users to free convert almost all HD videos and SD videos to QuickTime accepted formats on Mac with first rate quality.The input file formats covered by this powerful...
23.11 MB  
Macintosh Software  -  MacX Free Apple TV Video Converter 4.1.9
MacX Free Apple TV Video Converter is a 100% free video to Apple TV converter software which enables you to free convert most popular videos like AVCHD, MKV, M2TS, AVI, MPEG, WMV, FLV etc to Apple TV compatible format like MP4 format on Mac OS. In...
22.89 MB  
Macintosh Software  -  MacX Free DVD to PSP Converter for Mac 4.1.7
Looking for a solution to convert DVD to PSP for free? MacX Free DVD to PSP Converter for Mac is a 100% free DVD to PSP converter software which can assist you convert any DVD including copy protected DVDs to PSP supported MP4, H.264/MPEG-4 AVC...
36.26 MB  
Education  -  Sliding Down an Incline Plane Model 1.0
This interactive simulation shows a stone block lying at rest on an inclined plane. Initially, the component of gravity along the plane surface is exceeded by the force of static friction. The slope of the ramp can be increased or decreased,...
51.2 KB  
Education  -  MrAIC 1.4.4
MrAIC.pl is a Perl script for calculating AIC, AICc, BIC, and Akaike weights (for a review, see Burnham and Anderson, 2002) for nucleotide substitution models. Likelihood scores under different models are estimated using PHYML (Guindon and...
10.24 KB  
Education  -  HapEvolution 1.0
Complex diseases involve multiple genes with low penetration which may be distributed over the genome. Most of the current haplotype association methods are typically restricted in length and consist of alleles from contiguous SNPs. These...
1.61 MB  
Education  -  Three Charges 1.0
In this simulation, you can investigate the idea of the force between charged objects. Initially, the simulation sets up three charged objects, one at each corner of an equilateral triangle. The charges have different magnitudes - your job is to...
1.36 MB  
Education  -  AWclust 3.0
AWclust is easy to use non-parametric population structure analysis software written for R with a GUI interface. Just point and click and you will be on your way to discovering the important cluster information in your SNP data sets.
20.48 KB