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Description:

phenoapt 0.1.6

phenoapt

Phenotype-based Gene Prioritization, modelled using Graph Embedding techniques
This project contains the python client API library.

Installation
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

Features

Rank by genes or diseases
Optional phenotype weights can be supplied

Command line usage
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.

Code usage
See jupyter notebook example

History
0.1.0 (2020-09-06)

First release on PyPI.