Phenotype-based Gene Prioritization, modelled using Graph Embedding techniques
This project contains the python client API library.
You install phenoapt with pip:
pip install phenoapt
Or, if you prefer, clone the git repo and install from source:
git clone https://github.com/phenoapt/phenoapt.git cd phenoapt python setup.py install
- Rank by genes or diseases
- Optional phenotype weights can be supplied
An example of top 10 gene rankings given phenotypes and weights:
$ phenoapt rank-gene -p 'HP:0001193,HP:0001231,HP:0002999,HP:0003621' -w '1,2,2,1' -n 10
rank score entrez_id gene_symbol
------ ------- ----------- -------------
1 72.5097 EZ:8200 GDF5
2 73.8103 EZ:2697 GJA1
3 79.5231 EZ:51360 MBTPS2
4 85.5202 EZ:2316 FLNA
5 86.5767 EZ:10682 EBP
6 86.7231 EZ:8481 OFD1
7 86.9275 EZ:4010 LMX1B
8 87.2089 EZ:3930 LBR
9 91.1848 EZ:4000 LMNA
10 92.2059 EZ:2273 FHL1
and similarly, disease rankings can be obtained like this:
$ phenoapt rank-disease -p 'HP:0001193,HP:0001231,HP:0002999,HP:0003621' -w '1,2,2,1' -n 10
rank score disease_id disease_name
------ ------- ------------ -------------------------------------------------------------------------------
1 63.2341 OMD:228900 FIBULAR HYPOPLASIA AND COMPLEX BRACHYDACTYLY
2 66.2116 OMD:215140 GREENBERG DYSPLASIA; GRBGD
3 66.3988 OMD:161200 NAIL-PATELLA SYNDROME; NPS
4 71.6026 OMD:308205 IFAP SYNDROME WITH OR WITHOUT BRESHECK SYNDROME
5 73.3633 OMD:302960 CHONDRODYSPLASIA PUNCTATA 2, X-LINKED DOMINANT; CDPX2
6 73.3904 OMD:135900 COFFIN-SIRIS SYNDROME 1; CSS1
7 74.5251 OMD:228930 FIBULAR APLASIA OR HYPOPLASIA, FEMORAL BOWING AND POLY-, SYN-, AND OLIGODACTYLY
8 75.0786 OMD:611816 TEMPLE-BARAITSER SYNDROME; TMBTS
9 75.1829 OMD:228520 FIBROCHONDROGENESIS 1; FBCG1
10 78.0241 OMD:609945 OMD:609945
For more information about tool usage, run phenoapt with --help.