Question: Non sc-RNA-Seq and Cell Type
gravatar for ldyer2006
13 months ago by
ldyer200630 wrote:

Hi all,

Hope you can help me with this one as I'm having a bit of trouble.

Currently, I'm doing an experiment which has RNA-Seq data on a lot of samples from a differentiation procedure under a few different conditions.

I'd be very interested in looking into what cell types each condition/time combination clustered into. So far, I have found Sincera (R package) to work pretty well. The results line up with our observed phenotype quite well, but not perfectly. It would be really great if we could generate another set of results with a different method/pipeline and examine those, too, as a comparison.

I have so far looked into AUCell and EWCE, another set of R packages, however, these are both very poorly documented (Or perhaps my reading comprehension is just falling down this late on a Friday) and I am not confident they can achieve the kind of "cell type set enrichment" that I want.

Does anybody know of any tools which are designed to do this in a simple way, such as with Sincera (Filter, normalise, analyse and get results without a fuss)? Or perhaps anyone has a lot of experience with EWCE or AUCell and tell me if I'm barking up the wrong tree by trying to apply them to non-scRNA-Seq data. The cell types I'm interested in are not within the brain, which seems to be what the best tools focus on.

Thanks a lot for your time, any attention/help very appreciated.

rna-seq cell • 352 views
ADD COMMENTlink modified 13 months ago by shoujun.gu310 • written 13 months ago by ldyer200630

Can you specify whether you're working with bulk or single-cell RNA-seq? SINCERA was developed for scRNA-seq, but your title states "non-scRNA-seq".

ADD REPLYlink written 13 months ago by Friederike5.8k

Are you trying to do bulk RNA-seq data deconvolution? If yes, then you need smth like this - Depending on your answer I might suggest few more, but I'm not sure if you just want to check what is the most similar cell type to the particular RNA-seq sample or if you want to get cell type composition of your RNA-seq sample.

ADD REPLYlink written 13 months ago by aln290
gravatar for
13 months ago by
shoujun.gu310 wrote:

R: Seurat

Python: Scanpy

Both well documented.

ADD COMMENTlink modified 13 months ago • written 13 months ago by shoujun.gu310
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 875 users visited in the last hour