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Store and access gene expression datasets and gene definitions.

Project description

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              | ExonLength |
 |--------------------|-------------|----------|------------|------------------------------|----------------------------------|------------------------|-------------------------|------------|
 | ENSG00000183625    | HomoSapiens | 1232     | CCR3       | CC-CKR-3|CD193|CKR3|CMKBR3   | chemokine (C-C motif),receptor 3 | 1242.5                 | ENSMUSG00000035448:Ccr3 | 3568.0     |
 | ENSMUSG00000035448 | MusMusculus | 12771    | Ccr3       | CC-CKR3|CKR3|Cmkbr1l2|Cmkbr3 | chemokine (C-C motif),receptor 3 | 3273                   | ENSG00000183625:CCR3    | 3273.0     |

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

Changes

  • v0.1.x - Initial release with minor adjustments to test pypi and github upload/download.
  • v0.6.2 - Added a new column ‘ExonLength’ to the data.

License

MIT License

Project details


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