Metadata-Version: 2.1
Name: footprint_tools
Version: 1.1.3
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/1.1.3.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.
        
        Footprint-tools detects footprints 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 (>=3.5) and depends on the following additional
        packages:
        
        * cython (>=0.22)
        * numpy (>=1.10)
        * scipy (>=0.16)
        * statsmodels
        * pysam
        * genome_tools (1.0.1) (http://www.github.com/jvierstra/genome_tools)
        * pyfaidx (https://github.com/mdshw5/pyfaidx)
        * pwlf (https://github.com/cjekel/piecewise_linear_fit_py)
        
        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
        ```
        
        ## Documentation & usage
        
        User manual, API and examples can be found [here](http://footprint-tools.readthedocs.io)
        
        ## Citation
        
        [Vierstra2020](https://doi.org/10.1101/2020.01.31.927798) Global reference mapping and dynamics of human transcription factor footprints. Vierstra J *et al.* (2020) bioRxiv.
        
Keywords: genomic footprints,bioinformatics
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 :: 2.7
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/markdown
