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biolab / orange3-single-cell

🍊🔬 Orange add-on for gene expression of single cell data
https://singlecell.biolab.si/
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Marker genes #367

Closed YuriB85 closed 4 years ago

YuriB85 commented 4 years ago

Hi, I am following the example "Exploring the Fruit Fly Olfactory System" and using the "Marker genes" widget I cannot retrieve acj6. image It seems that the only organisms I can choose from are "Human" and "Mouse". I tried to use the "Databases Update" but without any luck. Should I import these marker genes manually from Li et al. (2017)? Thank you in advance.

BlazZupan commented 4 years ago

Thank you for your writing. Reported is not a bug. Marker Genes widgets presents marker genes from two databases, CellMarker and Panglao that currently include only markers for human and mouse. To include marker genes from some other source, including the publication, create your own data file with genes and cell types, read the file with File widget, and pass them through Genes widget to obtain associated Entrez IDs.

YuriB85 commented 4 years ago

Hello, I was wondering whether you are planning to add any functionality in scOrange to handle TCGA datasets. Specifically, I am interested in downloading gene expression datasets, as well as clinical annotation files and perform differential gene expression analyses between tumor patients and healthy control and to conduct survival analyses to test the prognostic value of particular gene panels. Many thanks in advance.

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ajdapretnar commented 4 years ago

@YuriB85 It is best if you open such questions as a new issue and tag it with 'Question' or something similar.