Maryam-Haghani

Error in list method

8

Hi, I am using _**list**_ command to get the sub-trees for 3 taxa of _[11050, 11103, 11108]_, the result is different for different orders of these taxa. i.e.: When I...

Different results when restricting background set to only include genes with at least one annotation term

1

Hi, I performed the enrichment analysis using my background set, and repeated it restricting the background set to only include genes with at least one annotation term (based on annotation...

An example of GOEA with Uniprots

6

Hi, I have noticed in the paper that we can use GPAD format from European Bioinformatics Institute’s FTP site for Gene Ontology Enrichment Analysis instead of NCBI's GAF format: >...

Hi! I am confused about how your [code](https://github.com/j3xugit/RaptorX-3DModeling/blob/bf175f72bdfd75cbb15676475f3eef2a112084d4/BuildFeatures/Helpers/CalcMeff.py) calculates Meff in the [a3m format](https://yanglab.nankai.edu.cn/trRosetta/msa_format.html#a3m) when 'gaps aligned to inserts' are omitted. Specifically, it appears that the code treats matches (uppercase...