Previously loaded in GSEA. Method3: Drag and drop files to GSEA 4. Either drag or drop all three files that you downloaded in step 2.a or browse the location where you saved the files and upload them in GSEA. Click on Run GSEA tab from left side menu panel. The first section is. Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq) - xzhoulab/iDEA. 15) Install GSEA. Go to the GSEA page Register Login In menu, choose Downloads Go to the javaGSEA Java Jar file section and download the gsea-3.0.jar file and save in your Documents folder (do not leave it in the “Downloads”folder). To run GSEA during the workshop, you must use the command line. Second, when I opened the downloaded.jnlp file, GSEA does open fine, but when the Load Data button is clicked on, there is no pop up window for input files. I have the latest Java (9.0) installed on my Mac (OS X 10.10). Any discussion on this will be appreciated!
UNLABELLED: Gene Set Enrichment Analysis (GSEA) is a computational method that assesses whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. We report the availability of a new version of the Java based software (GSEA-P 2.0) that represents a major improvement on the previous release through the addition of a leading edge analysis component, seamless integration with the Molecular Signature Database (MSigDB) and an embedded browser that allows users to search for gene sets and map them to a variety of microarray platform formats. This functionality makes it possible for users to directly import gene sets from MSigDB for analysis with GSEA. We have also improved the visualizations in GSEA-P 2.0 and added links to a new form of concise gene set annotations called Gene Set Cards. These additions, as well as other improvements suggested by over 3500 users who have downloaded the software over the past year have been incorporated into this new release of the GSEA-P Java desktop program.
AVAILABILITY: GSEA-P 2.0 is freely available for academic and commercial users and can be downloaded from http://www.broad.mit.edu/GSEA
TeX Live - Quick install
If you don't want to bother reading the full installdocumentation and just want to install everything in TeX Live, on aUnix-like system, a minimal recipe follows.
- Special considerations for Windows aredescribed separately.
- For MacOSX (aka macOS), we recommend installing MacTeX, which contains all of TeX Live (and a fewMac-specific additions).
- Cygwin users can follow the instructions for Unix-like systems, butmake sure you have the Cygwin prerequisitesbefore beginning the installation.
Pre-install: download, cleanup
![Gsea Gsea](/uploads/1/2/6/5/126588134/990837709.png)
A separate page describes various ways toacquire the software. It boils down to either getting the DVD froma TeX user group (ideally by becoming a member), or downloading in variousways. Except on Windows, your system must provide a standard Perlinstallation with the usual core modules. (For Windows, TeX Live comeswith its own Perl.)
If you're re-installing after a previous attempt, be sure tocompletely remove your failed installation. By default, this would bein these two directories (on Unix-like systems):
Running the installer
You do not need to be root (administrator on Windows) to install,use, or manage TeX Live. Indeed, we recommend installing it as a normaluser, except perhaps on MacOSX, where it's conventional to install asadministrator. (Some informationabout shared installations.) As always, you need to have permissionto write into the destination directory, but TeX Live itself does notcare if you are root or not.
So, once you have the software, run the install-tl script to install (on Windows,install-tl-windows), like this:
To change the installation directories or other options, read theprompts and instructions. The default is to install into paralleldirectories named by the release year, so that any given release can berun independently, merely by adjusting the search path.
Gsea Install
Interfaces to the installer: text, GUI, batch
The installer supports text, graphical, and batch interfaces:
- install-tl -gui text
uses a plain text interface(command line) mode. This is the default on Unix-like systems othe thanMacs. - install-tl -gui
is the default graphical GUI. Atstartup it offers very few options, but there is an‘Advanced’ button for more configurability. This is thedefault on Windows and on Macs. It requires Tcl/Tk, which is present onMacs and is provided for Windows. - install-tl --profile=profile
does a batch(unattended) installation. To create such a profile file, it's easiest tostart with the tlpkg/texlive.profile file which the installerwrites at the end of any successful installation.
For information on all of the installer options, run install-tl--help, or see the install-tldocumentation page.
Gsea Software Download
Choosing a download host
It can take an hour or more to copy all the files, depending on theinstallation method. If you are downloading over the network, bydefault a nearby CTAN mirror isautomatically chosen. If you have problems, we recommend choosinga specific mirror and then runinstall-tl --location http://mirror.example.org/ctan/path/systems/texlive/tlnetinstead of relying on the automatic redirection.
Post-install: setting PATH
After the installation finishes, you must add the directory of TeXLive binaries to your PATH—except on Windows, where the installertakes care of this. For example:
PATH=/usr/local/texlive/2020/bin/x86_64-linux:$PATH
Use the syntax for your shell, your installation directory, and yourbinary platform name instead of x86_64-linux.
PATH=/usr/local/texlive/2020/bin/x86_64-linux:$PATH
Use the syntax for your shell, your installation directory, and yourbinary platform name instead of x86_64-linux.
If you have multiple TeX installations on a given machine, you needto change the search path to switch between them—except on MacOSX.
Post-install: setting the default paper size
The default is to configure the programs for the A4 paper size. Tomake the default be 8.5x11 letter-size paper, you can use the‘o’ menu option before i(nstalling), or runtlmgr paper letter after installation (and aftersetting your PATH).
Gsea Mouse Gene Set
Testing
After a successful installation, please try processing simple testdocuments, such as latex small2e.
If you're looking for a front-end with which to edit files: TeX Liveinstalls TeXworks on Windows, and MacTeXinstalls TeXShop.In any case, a plethora of dedicatedTeX editors are available. Furthermore, any plain text editor willwork.
Getting updates
If you want to update packages from CTAN after installation, seethese examples of using tlmgr.This is not required, or even necessarily recommended; it's up to you todecide if it makes sense to get continuing updates in your particularsituation.
Typically the main binaries are not updated in TeX Live between majorreleases. If you want to get updates for LuaTeX and other packages andprograms that aren't officially released yet, they may be available inthe TLContrib repository, oryou may need to compile the sources yourself.
Reporting problems
Gsea Tutorial
Please see the known issues page for bugreporting info. And please check the documentation.