Metadata-Version: 1.1
Name: genedataset
Version: 0.2
Summary: Store and access gene expression datasets and gene definitions.
Home-page: https://github.com/jarny/genedataset
Author: Jarny Choi
Author-email: jchoi@wehi.edu.au
License: UNKNOWN
Description: genedataset
        ===========
        
        **genedataset** is a package to store and access gene expression
        datasets and gene definitions. It consists of two main classes, geneset
        and dataset.
        
        geneset
        -------
        
        geneset stores gene information combined from both Ensembl and
        NCBI/Entrez (mouse and human only), so that you can query it:
        
        ::
        
            $ gs = geneset.Geneset().subset(queryStrings='ccr3')
            $ print gs.geneIds()
             ['ENSG00000183625', 'ENSMUSG00000035448']
            $ gs.dataframe()
             | EnsemblId          | Species     | EntrezId | GeneSymbol | Synonyms                     | Description                      | MedianTranscriptLength | Orthologue              |
             |--------------------|-------------|----------|------------|------------------------------|----------------------------------|------------------------|-------------------------|
             | ENSG00000183625    | HomoSapiens | 1232     | CCR3       | CC-CKR-3|CD193|CKR3|CMKBR3   | chemokine (C-C motif),receptor 3 | 1242.5                 | ENSMUSG00000035448:Ccr3 |
             | ENSMUSG00000035448 | MusMusculus | 12771    | Ccr3       | CC-CKR3|CKR3|Cmkbr1l2|Cmkbr3 | chemokine (C-C motif),receptor 3 | 3273                   | ENSG00000183625:CCR3    |
        
        dataset
        -------
        
        dataset can store gene expression data so that it can be queried. The
        stored data consists of expression values (microarray and rna-seq) and
        sample data packaged into HDF5 format.
        
        ::
        
            $ ds = dataset.Dataset("genedataset/data/testdataset.h5")
            $ ds
             <Dataset name:testdata species:MusMusculus, platform_type:microarray>
            $ ds.expressionMatrix()
             | probeId | s01  | s02  | s03  | s04  |
             |---------|------|------|------|------|
             | probe1  | 3.45 | 4.65 | 2.65 | 8.23 |
             | probe2  | 5.54 | 0.00 | 1.43 | 6.43 |
             | probe3  | 0.00 | 0.00 | 4.34 | 5.44 |
            $ ds.sampleTable()
             | sampleId | celltype | tissue |
             |----------|----------|--------|
             | s01      | B1       | BM     |
             | s02      | B1       | BM     |
             | s03      | B2       | BM     |
             | s04      | B2       | BM     |
        
        Contact
        -------
        
        Jarny Choi, Walter + Eliza Hall Institute
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        -  e-mail: jchoi@wehi.edu.au
        
        Changes
        -------
        
        -  v0.1.x - Initial release with minor adjustments to test pypi and github upload/download.
        
        License
        -------
        
        `MIT License`_
        
        .. _MIT License: LICENSE.txt
        
Keywords: gene microarray rna-seq
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
