Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.
The online documentation for the module can be found here.
- Python >= 3.6
- R >= 3.6.0
- pip
- wget
- build-essential (make, g++, cmake)
- git
- libgit2
Install it using pip to use it as module:
pip install git+https://github.com/PhosphorylatedRabbits/cosifer@masterOr install it via pip after cloning (suggested for development):
cd cosifer
pip install -U -e .To install some of the requirements a compiler supporting OpenMP is needed. We suggest to use [brew] to install it and use it for the compilation as follows:
brew install gcc # this might take time
CC=/usr/local/bin/g++-9 pip install git+https://github.com/PhosphorylatedRabbits/cosifer@masterThe COSIFER executable accept the following arguments:
usage: cosifer [-h] -i FILEPATH -o OUTPUT_DIRECTORY [--standardize]
[--no-standardize] [--samples_on_rows] [--sep SEP]
[--fillna FILLNA] [--header HEADER] [--index INDEX]
[--methods METHODS] [--combiner COMBINER]
[--gmt_filepath GMT_FILEPATH]
Run COSIFER to perform network inference on given data.
optional arguments:
-h, --help show this help message and exit
-i FILEPATH, --filepath FILEPATH
path to the data.
-o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
path to the output directory.
--standardize flag that indicates whether to perform
standardization. Defaults behaviour is to standardize
the data.
--no-standardize flag that indicates whether to suppress
standardization. Defaults behaviour is to standardize
the data.
--samples_on_rows flag that indicates that data contain the samples on
rows. Defaults to False.
--sep SEP separator for the data. Defaults to .
--fillna FILLNA fill NAs with a given value. Defaults to 0..
--header HEADER header index in the data. Defaults to 0.
--index INDEX column index in the data. Defaults to None, a.k.a., no
index.
--methods METHODS methods which should be used for network inference. If
no methods are passed, it defaults to the following
set of methods: ['pearson', 'spearman', 'aracne',
'mrnet', 'clr', 'funchisq']
--combiner COMBINER method used for consensus network inference. Defaults
to: summa
--gmt_filepath GMT_FILEPATH
optional GMT file to perform inference on multiple
gene sets.In the folder examples, you can find applications of COSIFER consensus network inference.
The COSIFER web-service has been deprecated in favour of the python package hosted in this repository. Please check the examples to use COSIFER in your research.
If you use COSIFER in you research please cite:
@article{10.1093/bioinformatics/btaa942,
author = {Manica, Matteo and Bunne, Charlotte and Mathis, Roland and Cadow, Joris and Ahsen, Mehmet Eren and Stolovitzky, Gustavo A and Martínez, María Rodríguez},
title = "{COSIFER: a python package for the consensus inference of molecular interaction networks}",
journal = {Bioinformatics},
year = {2020},
month = {11},
issn = {1367-4803},
doi = {10.1093/bioinformatics/btaa942},
url = {https://doi.org/10.1093/bioinformatics/btaa942},
note = {btaa942},
eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa942/34088187/btaa942.pdf},
}
