Metadata-Version: 2.1
Name: SpliceV
Version: 0.1.6.10b0
Summary: Visualize splice junctions, backsplice junctions (circleRNA) and coverage from RNA-Seq datasets
Home-page: https://github.com/flemingtonlab/SpliceV
Author: Nathan Ungerleider
Author-email: nungerle@tulane.edu
License: UNKNOWN
Description: # SpliceV #
        Visualize coverage, canonical, and backsplice junctions.
        
        ![Example plot](https://github.com/flemingtonlab/SpliceV/blob/master/etc/example.png)
        
        ## Documentation ##
        See https://splicev.readthedocs.io/en/master/
        
        ## Example pipeline ##
        See https://github.com/flemingtonlab/SpliceV/blob/master/docs/example.pdf
        
        This will generate figure 1B and 1C from our manuscript (DOI pending)
        
        ## Requirements ##
        SpliceV works with Python 2.7 and 3.0+.
        ## Dependencies ##
        * Matplotlib
        * Numpy
        * pysam
        ## Installation ##
        To install SpliceV:
        
        ```
        pip install SpliceV
        ```
        
        Or:
        
        ```
        git clone https://github.com/flemingtonlab/SpliceV.git
        ```
        
        ## Example ##
        To run the example dataset:
        
        ```
        git clone https://github.com/flemingtonlab/SpliceV.git 
        
        cd SpliceV/example 
        
        python ../bin/SpliceV -b example.vta1.bam -gtf vta1.gtf -sj example.canonical.bed -bsj example.circles.bed -g VTA1 -f 3 -is 3
        
        ```
        
        The sample data comes from Akata cells (a B Cell Lymphoma line) that were treated with the exonuclease RNase R prior to sequencing. RNase R exclusively digests RNA with a free end, helping enrich circularized RNA abundance in the sample. 
        
        These example commands will generate the following plot:
        ![User example plot](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1.png)
        
        This plot reveals a prominant circle from exon 2 through exon 4 (evidenced by the back-splice junction reads which are plotted as curves below the axis. This is also demonstrated by the higher level of coverage in exon 2-4, shown by the relative intensity of color).
        
        ![User example plot explained](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1_explained.png)
        
        The major circularized isoform (exons 2-4; another less prevalent circle appears to include exon 5) is isolated below:
        
        
        ![User example circle](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1_circ.png)
        
        ## Authors ##
        Created by Nathan Ungerleider and Erik Flemington
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >=2.7,>=3
Description-Content-Type: text/markdown
