enter image description hereThere is a scRNA dataset on Glioblastoma from 10xgenomics. Unfortunately, there seems to be no research paper related to that data.

Question 0 : May be there is paper ? How to find it ? I am not familiar with 10xgenomics - may be there is some standard way to find papers related to their datasets ? May be their data also placed in GEO database, then what is GSE-id ?

Any way, we can see several clusters in the data (see figure above or switch to tab 'analysis' at the link above).

Question 1: What can be biological interpretation of these clusters ? I would expect cancer cells to be more homogeneous, but here we see several well-separated clusters, probably something like that has been already discussed in the literature ?


That dataset has been placed on kaggle https://www.kaggle.com/reminho/human-glioblastoma-dataset by enthusiast and one can find several notebooks in R and Python to play with it. Clusters are also present there.

In general there are many datasets/notebooks/people related to bioinformatics on kaggle, it is quite convenient platform for everything related to data science - data sharing, data processing on their servers for free (like colab), commenting on the works of others and so on. It seems it would be useful to create bioinformatics "community" on kaggle (there are already 12 other "communities") if you find that idea - useful please share your comments/make upvote/show yourself at: https://www.kaggle.com/general/203136

  • $\begingroup$ I actually do not think cancers are homogeneous. There can be cancer cells, normal cells, various immune cells in cancer tissue. So it is not surprising to see these many clusters, it may be helpful to try to find markers for different clusters and identify the cell type. $\endgroup$
    – Phoenix Mu
    Dec 18, 2020 at 23:30


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