Metadata-Version: 2.1
Name: footprint-tools
Version: 1.3.4
Summary: Genomic footprint detection
Home-page: https://github.com/jvierstra/footprint-tools
Author: Jeff Vierstra
Author-email: jvierstra@altius.org
License: GPL-3.0-or-later
Download-URL: https://github.com/jvierstra/footprint-tools/archive/v1.3.4.tar.gz
Description: # footprint-tools: *de novo* genomic footprint detection 
        
        footprint-tools is a python module for *de novo* detection of genomic footprints from DNase I data 
        by simulating expected cleavage rates using a 6-mer DNase I cleavage preference model combined
        with density smoothing. Statistical significance of per-nucleotide cleavages
        are computed from a series emperically fit negative binomial distribution.
        
        ## Requirements
        
        ``footprint-tools`` requires Python 3.6+
        
        We also recommend these non-Python analysis tools:
        
        * [samtools](http://www.htslib.org/)
        * [BEDOPS](http://bedops.readthedocs.io)
        * [kentUtils](https://github.com/ucscGenomeBrowser/kent/tree/master/src/utils)
        
        ## Installation
        
        To install the latest release, type:
        ```
        pip install footprint-tools
        ```
        
        If you run into errors, try installing footprint-tools in a conda environment (using the YAML file provided):
        ```
        # Clone repository
        git clone https://github.com/jvierstra/footprint-tools.git
        
        # Switch to devel branch; note that “master” branch is still “old” code
        git checkout devel
        
        # Create conda enviroment from config YAML file
        cd footprint-tools
        conda env create -f conda-env.yml
        
        # Activate conda environment
        conda activate footprint-tools
        
        # Run commands
        ftd --version
        ftd {commands}
        ```
        
        ## Documentation & usage
        
        User manual, API and examples can be found [here](http://footprint-tools.readthedocs.io)
        
        ## Citation
        
        [Vierstra2020](https://doi.org/10.1038/s41586-020-2528-x) Vierstra, J., Lazar, J., Sandstrom, R. *et al.* Global reference mapping of human transcription factor footprints. *Nature* **583**, 729–736 (2020)
        
Keywords: genomic footprints,bioinformatics,chromatin,transcription factors,dnase
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Description-Content-Type: text/markdown
