A package for generating curation sheets for rationally enriching a BEL graph using INDRA and PyBEL.
Project description
A package for generating curation sheets for rationally enriching a BEL graph.
If you find bel_enrichment useful in your work, please consider citing [1]:
Additionally, this package also heavily builds on INDRA [2] and PyBEL [3].
Installation 
bel_enrichment can be installed from PyPI with the following command:
$ pip install bel_enrichmentThe latest version can be installed from GitHub with:
$ pip install git+https://github.com/bel-enrichment/bel-enrichment.gitUsage
Generate a folder full of curation sheets based on the given BEL graph that has been pre-compiled by PyBEL. Use --info-cutoff to specify the minimum information density cutoff. 1.0 means that the node has no edges, .5 means one edge, and so on. Use --belief-cutoff to specify the minimum belief score from INDRA for adding the statement to the sheet. Higher belief means the more chance a statement is already right.
$ bel-enrichment make_sheet zhang2011.bel --directory ~/Desktop/zhang-enrichmentGenerate a ranking for genes based on the information content in a given BEL graph that has been pre-compiled by PyBEL.
$ bel-enrichment ranks zhang2011.belReferences
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file bel_enrichment-0.0.3.tar.gz.
File metadata
- Download URL: bel_enrichment-0.0.3.tar.gz
- Upload date:
- Size: 15.3 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.0.1 requests-toolbelt/0.9.1 tqdm/4.32.2 CPython/3.7.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | a549e36bb021b5d540f86f700b309e1a7eb2c1f7ba96cd460b7d80a1d86179ee |
|
| MD5 | 9ad150de1fe99871c3ccbf355c3a3415 |
|
| BLAKE2b-256 | 12995ca31c1c271e672b27a15e95eb2f0d178adb1c20d018b6d28febe575c41e |
Provenance
File details
Details for the file bel_enrichment-0.0.3-py3-none-any.whl.
File metadata
- Download URL: bel_enrichment-0.0.3-py3-none-any.whl
- Upload date:
- Size: 16.2 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.0.1 requests-toolbelt/0.9.1 tqdm/4.32.2 CPython/3.7.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | b733c962dac0eed0265acff45be4d9e9db1c407704e2f83a5c3c7e0e878dfe66 |
|
| MD5 | 59deff2c005814fc25bc7c419605f683 |
|
| BLAKE2b-256 | 9135e1fcb8f8623baa8816dd447131823c4e007f6a8537eaf3e7aa49df4b61f2 |
