OUTRIDER

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This adds the functionality to OUTRIDER to compute the FDR on subsets of genes of interest instead of all genes, and to retrieve the results table with that info included....

ischeller

controlForConfounders uses as much memory as available on machine

14

Thank you for this very helpful package. I've noticed this issue when moving my workflow over to a high performance computing cluster. Specifically, I try to run the exact same...

WGarrettJenkinson

Installation issues with R aarch64-apple-darwin20

2

I have an Apple M1 Pro Chip and I cannot install OUTRIDER. I was using another R version before, but once I changed to this R version, I cannot install...

ricorona

findEncodingDims Out-of-Memory Issues

5

Dear Gagneur Lab, I'm currently trying to determine the optimal q-value for my OutRider analysis. For which I'm using the following code: ``` # calculate optimal q encDimParams

lemdcock

Errors in the codes from pdf OUTRIDER - OUTlier in RNA-Seq fInDER

1

Dear Sir/Madam I was trying to run OUTRIDER with R following the instructions in the pdf file OUTRIDER - OUTlier in RNA-Seq fInDER, and got errors at the following steps:...

Paranchai

findEncodingDim issues

5

Dear Gagneur Lab, I'm using OutRider for aberrant gene expression analysis. However, I'm experiencing issues with the findEncodingDim function. I use the following code: ``` ### Pre-processing ### ods

lemdcock

I am working on epigenomic data to find outliers. I have over ~350K features. I requested for 15 cores but I keep getting the following error. Can I just use...

gk1610

findEncodingDim running issues

2

Hello, I am trying to implement the package for outlier detection and I am stuck on the `findEncodingDim` step. I looked into previous issues and solutions and implemented the following...

runjin326

Description of each column from results() function

1

This package is really useful, but I would suggest improving the documentation on the `results()` function. Some of the columns from the dataframe produced by results() are straightforward to understand,...

iaradsouza1

Validation data set not producing values concordant with manual

1

I've used OUTRIDER in my Thesis but have been advised that the very slight variability between the values I achieve and the values achieved in the OUTRIDER manual is a...

J-Lye