Downloaded over 20,000 times and cited in over 400 peer-reviewed publications. AltAnalyze has hundreds of active users and is being actively developed as an open-source project.

AltAnalyze recieves funding from NIH National Cancer Institute (R01CA226802).


: See our new manuscripts describing the AltAnalyze workflows ICGS2 and cellHarmony and their application, in new article in Nature.




Help Running AltAnalyze on Mac OS X

AltAnalyze is provided as pre-compiled binaries for the Mac OS X and Windows as a source code through PyPI and the GitHub repository (latest code). The pre-compiled versions help you avoid issues with installing and updating dependecies of which there are many in AltAnalyze.

If you are running on the pre-compiled Mac version and encounter an error, don't worry, the below should help you get through it.

What to do for "Unidentified Developer Warning"?
This issue is common for more recent MacOS X operating systems. Although we are working to resolve it there is a simple workaround described in this video.

What to do for "AltAnalyze Excutable Not Opening"?
This issue can be encountered on some Mac OS X machines but not others, but can be easily solved by selecting the alternative AltAnalyze program Alias Icon in the AltAnalyze program directory (named AltAnalyze, with an alias icon). This short cuts an issue with Mac OSX recognizing the right path to the binary and application folder. See this video for help.
What to do for "Mac OS X Critical Error Warning"?
If you reach this error while running AltAnalyze, it indicates a serious system incompatibility with the your current specific OS version and our software. This issue has been specific noted in Mac OS 10.14.6, in which applications built using the Tkinter graphical interface framework, frozen using the software py2app, result in a system error that will cause your computer to freeze and automatically restart. Below are suggestions if you encounter this issue. In AltAnalyze version 2.13.1, the software will automatically detect this version incommpatibility and direct the user to this page.


Option 1: upgrade your operating system.This issue was not observed prior to OS 10.14.6 or after, enhance, upgrading (or potentially down-grading) your OS should resolve.
null Option 2: run AltAnalyze on another machine. This issue does not affect PCs or other Mac operating system versions.
null Option 3: run AltAnalyze from source code or python distributions (requires python 2.7). A PyPI version of AltAnalyze is available using: pip install altanalyze
null Option 4: running AltAnalyze from a virtual machine (VM). Although this should not be necessary, the user can run AltAnalyze using a VM for another operating system. For example, Oracle VM VirtualBox is a free solution for running a VM on your machine.

We appoligize for any convienience. Feel free to contact us with questions at: