These tools are all available through a Web interface with no programming experience required. 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. I am not familiar with GenePattern, but quoting the website: Your settings could look similar to screenshot below, with the exception that you should probably set “Access CPA images via URL” to “No”Īfter running your CP pipeline, just start CellProfilerAnalyst, select the *.properties file and start exploring.ĭepending on your assays readout, you might also check out Genepattern.ĬellProfiler has an output option for this as well, you find it in the “ExportToSpreadsheet” module where you can “create a GenePattern GCT file”. You can use the ExportToDatabase module set to the SQLite optionĪdditionally, in the same module, check “create CellProfilerAnalyst properties file”. If that opens okay, I think you’ll need to upload the pipeline you use to create the properties file and an example image to run it on. Maybe you could download and try and open it just to exclude an installation issue. There’s an example properties file at the bottom of this page. 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.Īs wrote, lmurphy (Laura Murphy) May 20, 2019, 9:05pm 2. Conversely, during the run we have access to the. In both of these phases we have access to the image names, but not their dimensionality. CellProfiler insists on creating the properties file in the pre-run phase and the post-run phases. Hi I just recently started using CellProfilerAnalyst to get a grip on screening data that we got from 96/384well plates. To generate the properties file correctly, we need to know how many channels each selected image contains. If you create several files with the same name and different locale suffixes (for. In the New File dialog, type the filename with the corresponding extension. From the context menu of the target directory, choose New File. ![]() If you also want the CSVs, you can have BOTH ExportToDatabase and ExportToSpreadsheet many free database reader programs will also allow you to open the SQLite database and export each table as its own CSV. Right-click a directory where you would like to create the file. You can indeed also configure ExportToDatabase to make the properties file you’ll need for CPA. If you want to be able to use CPA, you’re right you’ll need some kind of database- if you don’t want to have to deal with tangling with your university/company/etc database infrastructure, you can use the ExportToDatabase module set to the SQLite option- an SQLite database is essentially just a “wrapper” around a bunch of spreadsheets, so you can run it locally on your hard drive. Do you want to extract something super simple like cell count, or something really complicated like a subtle change in cell shape? How comfortable are you (if at all) with tools like Python, MATLab, R, or do you have a colleague or friend who is comfortable with them who can help you out? All of these factor into what your personal best next step should be. “What next” is an excellent question, and really depends on your particular situation. First of all, congratulations on your pipeline!
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