-
Path:
`/api/expressions/{bel}/orthologs`
`{bel}` term example:
- `p(HGNC:AKT1)`
`{bel}` statement example:
- `p(HGNC:AKT1) => bp(GOBP:"apoptotic process")`
extra parameters
- `{namespace_preferenc…
-
Hello,
Thanks for developing such useful tools. I want to use AGORA with providing the orthologous groups files and not the trees; I have a question regarding these orthology groups. I used Orthofi…
-
Human SHH page shows annotated to 12 orthologs; mouse shh page is annotated to 13 orthologs; dog to 4 orthologs etc. This is a bit unfortunately not as useful as it could be. In all cases, we are prob…
-
I used orthogroups identified in OrthoFinder as input for HyPhy analyses. I am working with 27 species, and there are 2,592 orthogroups identified as single-copy in all species. To include more orthog…
-
Currently, downloading and storing resources is quite bare bones:
https://github.com/saezlab/liana-py/blob/main/liana/resource/_orthology.py
https://github.com/saezlab/liana-py/blob/main/liana/reso…
-
hi xgrau,
When I run this script to identify the ortholog of my gene tree, I got two issues:
First, I got one warning: possvm1/lib/python3.10/site-packages/ete3-3.1.2-py3.7.egg/ete3/evol/parser/co…
-
The Alliance of Genome Resources (AGR) is a consortium of the most highly-used model organisms (mouse, rat, worm, fly, zebrafish, yeast), and they have released their own set of ortholog assignments a…
-
Hello! Hope you are all doing well! For the output alignments (nucleotide.fasta, codon.fasta, and protein.fasta), what gene projections/orthology classes are included here? By that I mean, what does T…
-
In RTD documentation:
- Add docker as possible installation
- In installation, at the end, include commands for additional requirements for orthology and lineage:
pip install pyaln
pip install ncb…
-
Basic example (provided by Anushya):
http://panthertest2.usc.edu/services/ortholog/matchOrtho.jsp?format=json&organism=9606&targetOrganism=10090,9913,83333&geneInputList=brca1&orthologType=all
I…