Metadata-Version: 1.1
Name: seqcluster
Version: 0.99.9
Summary: Small RNA-seq analysis
Home-page: http://github.com/lpantano/seqcluster
Author: Lorena Pantano
Author-email: lpantano@iscb.org
License: MIT
Description: seqcluster
        ---------
        
        small RNA analysis from NGS data
        
        .. image:: https://travis-ci.org/lpantano/seqcluster.png?branch=master
            :target: https://travis-ci.org/lpantano/seqcluster.png?branch=master
            
        .. image:: https://badge.fury.io/py/seqcluster.svg
            :target: http://badge.fury.io/py/seqcluster
        
        .. image:: https://pypip.in/d/seqcluster/badge.png
            :target: https://pypi.python.org/pypi/seqcluster
        
        
        Cite
        ---------
        
        A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
        Pantano L1, Estivill X, Martí E. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.
        PMID: 21976421
        
        installation
        ---------
        
        `seqcluster-helper`_ provides 
        a python framework to run an entire pipelie for small RNA (miRNA + others).
        
        Install first bcbio-nextgen and cutadapter::
        
            wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
            bash Miniconda-latest-Linux-x86_64.sh -b -p ~/install/seqcluster/anaconda
            PATH = ~/install/seqcluster/anaconda/bin:$PATH
            conda install pip
            conda install -c https://conda.binstar.org/bcbio bcbio-nextgen
            pip install cutadapt
        
        If you need to install bedtools, samtools and star::
        
           git clone https://github.com/Homebrew/linuxbrew.git  ~/install/seqcluster/linuxbrew
           cd ~/install/seqcluster/linuxbrew/bin
           ln -s `which gcc gcc-4.4`
           PATH = ~/install/seqcluster/linuxbrew/bin:$PATH
           brew tab homebrew/science
           brew tab chapmanb/homebre-cbl
           brew install bedtools
           brew install samtools
           brew install star-rna
           
        
        Then you can get seqcluster::
        
            pip install seqcluster
        
        or the developement version::
        
            git clone https://github.com/lpantano/seqcluster
            cd seqcluster
            python setup.py install
        
        
        .. _seqcluster-helper: https://github.com/lpantano/seqcluster-helper/blob/master/README.md
        
        
        quick start
        ---------
        
        Complete tutorial here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences
        
        report
        ---------
        
        Seqcluster can create html report that looks like `this`_. That is a table of all cluster detected, and you 
        can go into each of them and get a complete `description`_.
        
        .. _this: https://rawgit.com/lpantano/seqcluster/master/data/examples_report/html/index.html
        .. _description: https://rawgit.com/lpantano/seqcluster/master/data/examples_report/html/1/maps.html
        
Keywords: RNA-seq miRNA snoRNA NGS
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
