Metadata-Version: 2.1
Name: mirtop
Version: 0.4.23
Summary: Small RNA-seq annotation
Home-page: http://github.com/mirtop/mirtop
Author: Lorena Pantano
Author-email: lorena.pantano@gmail.com
License: MIT
Description: # mirtop <img src="artwork/logo.png" width="80" height="80">
        
        [![](https://travis-ci.org/miRTop/mirtop.svg?branch=master)](https://travis-ci.org/miRTop/mirtop#)
        [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
        [![biorxiv](https://img.shields.io/badge/biorxiv-published-red.svg)](https://www.biorxiv.org/content/10.1101/505222v1)
        
        Command line tool to annotate with a standard naming miRNAs e isomiRs.
        
        This tool adapt the miRNA GFF3 format agreed on here: https://github.com/miRTop/mirGFF3
        
        Chat
        ----
        
        [Ask question, ideas](https://gitter.im/mirtop/Lobby#)
        [Contributors to code](https://gitter.im/mirtop/devel)
        
        Cite
        ----
        
        http://mirtop.github.io
        
        Contributing
        ------------
        
        Everybody is welcome to contribute, fork the `devel` branch and start working!
        
        If you are interesting in miRNA or small RNA analysis, you can jump into the incubator issue pages to propose/ask or say hi:
        
        https://github.com/miRTop/incubator/issues
        
        About
        -----
        
        Join the team: https://orgmanager.miguelpiedrafita.com/join/15463928
        
        Read more: http://mirtop.github.io
        
        Installation
        ------------
        
        ### Bioconda
        
        `conda install mirtop -c bioconda`
        
        ### PIP
        
        `pip install mirtop`
        
        ### develop version
        
        Thes best solution is to install conda to get an independent environment.
        
        ```
        wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
        
        bash Miniconda-latest-Linux-x86_64.sh -b -p ~/mirtop_env
        
        export PATH=$PATH:~/mirtop_env
        
        conda install -c bioconda pysam pybedtools pandas biopython samtools
        
        git clone http://github.com/miRTop/mirtop
        
        cd mirtop
        
        python setup.py develop
        ```
        
        Quick start
        -----------
        
        Read complete commands at: https://mirtop.readthedocs.org
        
        ```
        git clone mirtop
        cd mirtop/data
        mirtop gff --sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out sim_isomir.bam
        ```
        
        Output
        ------
        
        The `mirtop gff` generates the GFF3 adapted format to capture miRNA variations. The output is explained [here](https://github.com/miRTop/mirGFF3).
        
        Contributors
        ------------
        
        * [Lorena Pantano](https://github.com/lpantano) (Bioinformatic Core, Harvard Chan School, Boston, USA)
        * [Shruthi Bhat Bandyadka](https://github.com/sbb25) (Partners Personalized Medicine, Cambridge MA, USA)
        * [Iñaki Martínez de Ilarduya](http://www.germanstrias.org/technology-services/high-performance-computing/contact/)(HPC core, IGTP, Badalona, Spain)
        * Rafael Alis
        * [Victor Barrera](https://github.com/vbarrera) (Bioinformatic Core, Harvard Chan School, Boston, USA)
        * [Steffen Möller](https://github.com/smoe) (University of Rostock)
        * [Kieran O'Neill](https://github.com/oneillkza)
        * [Roderic Espin](Universitat Oberta de Barcelona)
        
        Citizens
        --------
        
        Here we cite any person who has contribute somehow to the project different than through code development and/or
        bioinformatic concepts.
        
        Gianvito Urgese,
        Jan Oppelt(CEITEC Masaryk University, Brno, Czech Republic),
        Thomas Desvignes,
        Bastian,
        Kieran O'Neill (BC Cancer),
        Charles Reid (University of California Davis),
        Radhika Khetani (Harvard Chan School of Public Health),
        Shannan Ho Sui (Harvard Chan School of Public Health),
        Simonas Juzenas(CAU),
        Rafael Alis (Catholic University of Valencia),
        Aida Arcas (Instituto de Neurociencias (CSIC-UMH)),
        Yufei Lin (Harvard University),
        Victor Barrera(Harvard Chan School of Public Health),
        Marc Halushka (Johns Hopkins University)
        
Keywords: RNA-seq miRNA isomiRs annotation
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
