Metadata-Version: 2.1
Name: SPLICE-q
Version: 1.0.0
Summary: SPLICE-q is a fast and user-friendly Python tool for genome-wide SPLICing Efficiency quantification
Home-page: https://github.com/vrmelo/SPLICE-q
Author: Verônica R Melo Costa, Julianus Pfeuffer, Annita Louloupi, Ulf A V Ørom, Rosario M Piro
Author-email: veronica.melocosta@gmail.com
License: GPL-2
Description: # SPLICE-q
        
        A Python tool for genome-wide **SPLI**cing **E**fficiency **q**uantification from RNA-seq data.
        
        [User Manual](https://github.com/vrmelo/SPLICE-q/wiki)
        
        ## Features
        - Quantification of individual intron splicing efficiencies from strand-specific RNA-seq data.
        - Sensitive to the overlap of genomic elements.
        - Fast and user-friendly.
        
        # Installation
        
        SPLICE-q can be installed from pip and from source.
        
        ## pip
        Using pip is the easiest way to install SPLICE-q.
        ```bash
         $ pip3 install SPLICE-q
        ```
        
        ## Development/install from source
        
        ```bash
         $ git clone https://github.com/vrmelo/SPLICE-q
         $ cd SPLICE-q
         $ pip3 install -e .
        ```
        
        Requirements
        
        - Python 3.6+
        - PySam
        - InterLap
        - NumPy
        - Rich
        
        Operating Systems
        - Linux, macOS, and Windows 10 Subsystem for Linux.
        ## Usage
        
        To run SPLICE-q with default parameters, it requires a BAM file and a genome annotation file provided by GENCODE or Ensembl (GTF):
        ```bash
        $ SPLICE-q.py -b file.bam -g annotation.gtf
        ```
        To specify an output file name and location: 
        
        ```bash
        $ SPLICE-q.py -b file.bam -g annotation.gtf -o outfile.tsv
        ```
        
        Need help?
        ```bash
        $ SPLICE-q.py -h
        ```
        or check our [User Manual](https://github.com/vrmelo/SPLICE-q/wiki).
        
        ## Citation
        
        TBA
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
