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IGS / gEAR

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
https://umgear.org
GNU Affero General Public License v3.0
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Primary analysis "Labeled tSNE" window missing for some datasets #498

Closed beamilon closed 1 year ago

beamilon commented 1 year ago

@jorvis @adkinsrs @songeric1107 Going to the single cell workbench and selecting "Primary analysis", I noticed that for some datasets, 2 windows appear: Find marker genes AND Labeled tSNE. For other datasets, only Find marker genes appears. Below are two examples. I don't know if it is a bug or if it is dataset dependent.

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jorvis commented 1 year ago

Bea -

I believe I can give the explanation here but can you please provide the title of the 2nd example posted so I can verify? There are 9 datasets which start with the part of the label that is visible.

beamilon commented 1 year ago

Single cell RNA-Seq analysis of embryonic mouse spiral ganglion neurons (Sanders & Kelley 2022)

jorvis commented 1 year ago

When a user uploads their dataset there are two types of pre-computed analysis they can include - tSNE/UMAP and cluster information. If the cluster information is present marker genes can be computed.

P2, mouse, scRNA-seq, cochlea (Hertzano/Ament) - Has both tSNE and clustering data uploaded Single cell RNA-Seq analysis of embryonic mouse spiral ganglion neurons (Sanders & Kelley 2022) - Has only UMAP

The interface reads whether these datasets have these attributes and only shows the available options.