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RiboDiff: Tool to detect changes in translational efficiency based on ribosome footprinting data

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Several warnings using the test-data

Dear Yi Zhong (@yizhong), After trying to run your tool and checked the opened/closed issues on GitHub while I was trying to solve why I was getting some errors/warnings, I...

evaesquinas avatar evaesquinas

Many genes with padj=NaN despite removing low-expressed genes

Dear Yi Zhong (@yizhong), I am trying to use `Ribodiff` with 6 samples of RNA-seq and 6 samples of Ribo-Seq (unpaired data), with 30560 genes. When I run the tool...

evaesquinas avatar evaesquinas

Python 2 -> 3?

2 comment

Python 2 nears EOL. Are there plans to migrate RiboDiff to Python 3?

rekado avatar rekado

Divide by zero error, even with test data

I've tested installing RiboDiff locally, and installing via conda. I consistently get this error when running on my data and on the provided test data. `/nobackup/cm13ijb/miniconda/envs/RiboDiff/lib/python2.7/site-packages/ribodiff/adjlik.py:14: RuntimeWarning: divide by zero...

IsabelBirds avatar IsabelBirds

Default for Dispdiff is wrongly documented

Hey guys - looks like the manual has the wrong default for the disp diff option: Text in the manual: ``` OPTIONAL: -d DISPDIFF Allow different dispersions for Ribo-seq and...

zslastman avatar zslastman

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RiboDiff: Tool to detect changes in translational efficiency based on ribosome footprinting data

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