Errors when starting SCOUTS

I can’t start SCOUTS on my computer! scouts does nothing!

Please check the installation troubleshooting section.

I can’t start SCOUTS-violins on my computer! scouts-violins does nothing!

Please confirm that you have installed the necessary dependencies. Then check the installation troubleshooting section.

About the SCOUTS workflow

What type of pre-processing does SCOUTS perform on my input?

By default, SCOUTS does not perform any pre-processing prior to analysing the input data. This means that transformations like data normalization and scaling should be performed by the user prior to using SCOUTS.

SCOUTS does, however, include a simple module for gating mass cytometry and scRNA-seq samples, should the user want to do so. Refer to How SCOUTS works for details.

My data is stored in multiple files. How do I use SCOUTS with it?

Ideally, you are able to merge your files into a single input file and use that to work with SCOUTS. When this is not possible, you can still use SCOUTS to run individual samples by passing one file at a time. This will not affect the output, as long as all the cells from one sample are together in one file. One side-effect of this method is that, in order to use the “control” option in the “Consider outliers using cutoff from” field, you need to make sure that the cells from the control sample are present in every file.

Does the output for non-outliers exclude both top and bottom outliers?

Yes. Even if you did not generate output files for bottom outliers, non-outliers are still considered as being “the population of cells that are not top outliers, nor bottom outliers”.


I have another question/suggestion/issue when using SCOUTS. How do I contact you?

You can contact us through our Github page. Check the authors section for more information. Also remember that you can use the Github issues to post about problems or suggestions for SCOUTS.

SCOUTS is working nicely, but can you implement X?

Maybe! Tell us more about it on the Github issues page :-)