Hi @Anna2303, I just recently started using CellProfilerAnalyst to get a grip on screening data that we got from 96/384well plates.
I must say I really like it a lot and I can definitely recommend it to give it a try, especially if you have data that was acquired in well plates.
As @bcimini wrote,
Additionally, in the same module, check "create CellProfilerAnalyst properties file".
Your settings could look similar to screenshot below, with the exception that you should probably set "Access CPA images via URL" to "No"
After running your CP pipeline, just start CellProfilerAnalyst, select the *.properties file and start exploring.
Depending on your assays readout, you might also check out Genepattern.
CellProfiler has an output option for this as well, you find it in the "ExportToSpreadsheet" module where you can "create a GenePattern GCT file".
I am not familiar with GenePattern, but quoting the website:
GenePattern provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. These tools are all available through a Web interface with no programming experience required.
Hope this helps!