Metadata-Version: 1.1
Name: GEOpurify
Version: 0.1
Summary: Making Gene Expression Omnibus data cleansing easy.
Home-page: https://github.com/biologos/GEOpurify
Author: Sasha Illarionov
Author-email: sasha.delly@gmail.com
License: MIT
Download-URL: https://github.com/biologos/GEOpurify/archive/0.1.tar.gz
Description: * GEOpurify
        /Atlas of tools making Gene Expression Omnibus data amicable to machine learning./
        
        ** Installation
        
        #+BEGIN_SRC sh
        pip install GEOpurify
        #+END_SRC
        
        ** Example Usage
        
        #+BEGIN_SRC python :results output org drawer
        from GEOpurify import GEOpurifier
        g = GEOpurifier()
        gds_df = g.gdspurify("GDS4376")
        #+END_SRC
        
        ** Methods
        
        *** ~filepurify(filepath, separation="\t")~
        
        Given a path to a standard table with GEO data, returns a dataframe
        with gene expression and GSM ids in separate columns.
        
        *** ~dirpurify(dirname)~
        
        Given a path to a directory with standard tables of data from GEO,
        applies ~filepurify~ and return a combined dataframe.
        
        *** ~gdspurify(gds_id, load_extra_features=False)~
        
        Given a GDS id, extracts data on a platform, platform organism,
        platform techonolgy type and sample organism used. If
        ~load_extra_features~ is set to ~True~, extra features are fetched
        from the GDS columns.
        
        Saves already processed tables corresponding to the GDS in the
        directory ~data/tmp~, while storing the raw GEO data in the directory
        ~data/raw~.
        
        *** ~gdspolypurify(self, gds_list_path, load_extra_features=False)~
        
        Given a path to a file listing GDS ids, each on a new line, applies
        ~gdspurify~ to each and combines all the data into one dataframe.
        
Keywords: GEO,bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
