Metadata-Version: 1.1
Name: genedataset
Version: 1.0.0a4
Summary: Store and access gene expression datasets and gene definitions.
Home-page: https://github.com/jarny/genedataset
Author: Jarny Choi
Author-email: jarnyc@unimelb.edu.au
License: UNKNOWN
Description-Content-Type: 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.
        
        Changes in version 1.0
        ----------------------
        
        Some significant changes have been made in this version: 1.
        “MedianTranscriptLength” property of Geneset has been replaced with
        “TranscriptLengths”, which holds a list of transcript lengths, one per
        transcript (eg. [2000,1530]). Note that the value contained is a string,
        so convert into a list of integers before using the value. 2. The Gene
        annotation has been upgraded to Ensembl version 88. 3. Dataset no longer
        supports microarrays, so it’s been simplified, so related methods are
        deprecated. 4. The package supports both python 3 and 2 - tested on
        2.7.14 and 3.6.3.
        
        Installation
        ------------
        
        .. code:: bash
        
            pip install genedataset
        
            # If this installs the old version 0.6 instead of the latest, explicitly specify the version:
            pip install genedataset==[latest_version_number]
        
        geneset
        -------
        
        geneset stores gene information combined from both Ensembl and
        NCBI/Entrez (mouse and human only), so that you can query it:
        
        .. code:: python
        
            from genedataset import geneset
            gs = geneset.Geneset().subset(queryStrings='ccr3')
            print(gs.geneIds())
             ['ENSG00000183625', 'ENSMUSG00000035448']
            gs.dataframe()
        
             | EnsemblId          | Species     | EntrezId | GeneSymbol | Synonyms                     | Description                      | TranscriptLengths                             | Orthologue              |
             |--------------------|:-----------:|---------:|-----------:|-----------------------------:|---------------------------------:|----------------------------------------------:|------------------------:|
             | ENSG00000183625    | HomoSapiens | 1232     | CCR3       | CC-CKR-3|CD193|CKR3|CMKBR3   | C-C motif chemokine receptor 3   | [2000, 1581, 400, 436, 212, 1284, 1201, 1786] | ENSMUSG00000035448:Ccr3 |
             | ENSMUSG00000035448 | MusMusculus | 12771    | Ccr3       | CC-CKR3|CKR3|Cmkbr1l2|Cmkbr3 | chemokine (C-C motif) receptor 3 | [3272]                                        | ENSG00000183625:CCR3    |
        
        dataset
        -------
        
        dataset can store gene expression data so that it can be queried. The
        stored data consists of expression values (usually rna-seq) and sample
        data packaged into HDF5 format.
        
        .. code:: python
        
            from genedataset import dataset
            ds = dataset.Dataset("genedataset/data/testdata.1.0.h5")
            ds
             <Dataset name:testdata 4 samples>
            ds.expressionMatrix()
        
             | featureId | s01  | s02  | s03  | s04  |
             |---------|------|------|------|------|
             | gene1  | 3.45 | 4.65 | 2.65 | 8.23 |
             | gene2  | 5.54 | 0.00 | 1.43 | 6.43 |
             | gene3  | 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     |
        
        Dataset creation example
        ------------------------
        
        Here is an example to create a Dataset file from text files. Once the
        file has been created, it can be accessed through the Dataset instance.
        The advantage of this is to store all related information for a dataset
        in one file, and gives you a python object that can be used for analyses
        and for application development.
        
        .. code:: python
        
            import pandas
            from genedataset import dataset
            attributes = {"name": "testdata",
                          "fullname": "Test Dataset",
                          "version": "1.0",
                          "description": "This dataset comes with the package for testing purposes.",
                          "expression_data_keys": ["counts","cpm"],
                          "pubmed_id": None,
                          "species": "MusMusculus"}
            samples = pandas.DataFrame([['B1', 'BM'], ['B1', 'BM'], ['B2', 'BM'], ['B2', 'BM']],
                                       index=['s01','s02','s03','s04'],
                                       columns=['celltype','tissue'])
            samples.index.name = "sampleId"
            counts = pandas.DataFrame([[35, 44, 21, 101], [50, 0, 14, 62], [0, 0, 39, 73]],
                                      index=['gene1', 'gene2', 'gene3'], columns=['s01', 's02', 's03', 's04'])
            counts.index.name = "geneId"
            cpm = pandas.DataFrame([[3.45, 4.65, 2.65, 8.23], [5.54, 0.0, 1.43, 6.43], [0.0, 0.0, 4.34, 5.44]],
                                   index=['gene1', 'gene2', 'gene3'], columns=['s01', 's02', 's03', 's04'])
            cpm.index.name = "geneId"
            dataset.createDatasetFile("/datasets", attributes=attributes, samples=samples, expressions=[counts,cpm])
        
        Contact
        -------
        
        Jarny Choi, University of Melbourne
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        -  e-mail: jarnyc@unimelb.edu.au
        
        Changes
        -------
        
        -  v1.0 - Major upgrade.
        -  v0.1.x - Initial release with minor adjustments to test pypi and
           github upload/download.
        
        License
        -------
        
        `MIT License`_
        
        .. _MIT License: LICENSE.txt
        
Keywords: gene expression dataset rna-seq
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
