Marker Genes

We provide access to two different databases (of marker genes):

• PanglaoDB

• CellMarker

Data is preprocessed in Orange readable format and it is hosted here.

To get marker genes we need access files on our http file server. We can use a tool that handles just that. Detailed explanation on how to use it can be found here.

Usage

>>> from Orange.data import Table
>>> from orangecontrib.bioinformatics.utils import serverfiles
>>> markers = serverfiles.localpath_download('marker_genes', 'panglao_gene_markers.tab')
>>> data = Table(markers)
>>> data
>>>
[[] {Mouse, CTRB1, Acinar cells, PanglaoDB, https://panglaodb.se/, ...},
 [] {Mouse, KLK1, Acinar cells, PanglaoDB, https://panglaodb.se/, ...},
 [] {Mouse, RBPJL, Acinar cells, PanglaoDB, https://panglaodb.se/, ...},
 [] {Mouse, PTF1A, Acinar cells, PanglaoDB, https://panglaodb.se/, ...},
 [] {Mouse, TRY4, Acinar cells, PanglaoDB, https://panglaodb.se/, ...},
 ...
]