Hong Zhang

I have made [some modifications](https://github.com/mt1022/scikit-ribo) of the scripts in `scikit_ribo` folder to use with fly genome, some of which are based on the comments of @mschatz, @drewjbeh and other users...

@drewjbeh, Sure. Here are some tips to run scikit-ribo for other genomes: - The scikit-ribo is design for analysis of yeast data, which does not have UTR annotation. In order...

Seems to be an issue of numpy 1.15. I came across the same error, which disappeared when the numpy was updated to 1.19.

The coordinates for human lncRNAs in bed and gff are still the same (both are 1-based in most recent release of RNAcentral: V9). In addition, some lncRNA annotations are present...

We didn't try this. Combined and adjusted p values are calculated in this [script](https://github.com/xryanglab/RiboCode/blob/e9d6cc345299e67df225ca831417ad5137a54814/RiboCode/detectORF.py). The code is hard for me to follow.