Evaluattion of Predictive CapabilitY for ranking biomarker candidates.
Project description
Citing:
EPCY: Evaluation of Predictive CapabilitY for ranking biomarker gene candidates. Poster at ISMB ECCB 2019: https://f1000research.com/posters/8-1349
Introduction:
This tool was developed to Evaluate Predictive CapabilitY of each gene (feature) to become a predictive (bio)marker candidates. Documentation is available via Read the Docs.
Requirements:
python3
(Optional) virtualenv
Install:
Using pypi:
pip install epcy
From source:
python3 -m venv $HOME/.virtualenvs/epcy
source $HOME/.virtualenvs/epcy/bin/activate
pip install pip setuptools --upgrade
pip install wheel
cd [your_epcy_folder]
# If need it
# CFLAGS=-std=c99 pip3 install numpy==1.17.0
python3 setup.py install
epcy -h
Usage:
General:
After install:
epcy -h
From source:
cd [your_epcy_folder]
python3 -m epcy -h
Generic case:
EPCY is design to work on any quantitative data, provided that values of each feature are comparable between each samples (normalized).
To run a comparative analysis, epcy pred need two tabulated files:
# Run epcy on any normalized quantification data
epcy pred -d ./data/small_for_test/design.tsv -m ./data/small_for_test/log_normalized_matrix.tsv -o ./data/small_for_test/EPCY_output
# If your data are normalized, but require a log2 transforamtion, add --log
epcy pred --log -d ./data/small_for_test/design.tsv -m ./data/small_for_test/normalized_matrix.tsv -o ./data/small_for_test/EPCY_output
# If your data are not normalized and require a log2 transforamtion, add --norm --log
epcy pred --norm --log -d ./data/small_for_test/design.tsv -m ./data/small_for_test/matrix.tsv -o ./data/small_for_test/EPCY_output
# Different runs might show small variations.
# To ensure reproducibility set a random seed, using --randomseed
epcy pred -d ./data/small_for_test/design.tsv -m ./data/small_for_test/normalized_matrix.tsv -o ./data/small_for_test/EPCY_output --randomseed 42
epcy pred -d ./data/small_for_test/design.tsv -m ./data/small_for_test/normalized_matrix.tsv -o ./data/small_for_test/EPCY_output2 --randomseed 42
diff ./data/small_for_test/EPCY_output/predictive_capability.xls ./data/small_for_test/EPCY_output2/predictive_capability.xls
More documentation is available via Read the Docs.
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