ecotyper

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CIBERSORTx integration fails

2

Hello there once more :-) As I am aiming to become a regular customer, I have yet again a new issue 😄. Technically it's a CIBERSORTx issue not an EcoTyper...

NoahHenrikKleinschmidt

Tutorial 4 - Warning: Only 0 genes are available

14

Dear Ecotyper team, I tried to run Tutorial 4 - de novo discovery of Cell State and Ecotypes in bulk expression data - with my own bulk RNAseq data. After...

VerenaPass

How to apply for a Token of CIBERSORTx for docker ？

1

We're trying to run a big data in CIBERSORTx. We need the Token of CIBERSORTx for docker images. And we have asked for the Token from the website，but it's still...

liuyu999

scRNA Discovery step2 aborts after `state_discovery_scRNA_distances`

3

Hello there, This is a follow-up to my earlier issue that I self-diagnosed and is closed now. So, after a lot of diagnosing I found that step 2 (which has...

NoahHenrikKleinschmidt

Hi @BALuca and Team, I used CODEFACS for deconvolution and trying to use its output as an input for Ecotyper using tutorial_6. As recommended I used all the genes and...

biobug16

Question about normalized scaled matrix

1

Hello I am trying out Ecotyper to analyze single cell data and I read that it needs a normalized matrix I have used Scanpy and the following steps sc.pp.normalize_total(adata,target_sum=1e4) #...

seigfried

Tutorial 4 / scRNA Discovery / When to adjust Jaccard matrix p-value cutoff?

1

We have a scRNA dataset where we've had difficulty discovering ecotypes with EcoTyper when using a jaccard pval cutoff of 0.05. I'm considering loosening the Jaccard p-value cutoff -- in...

semenko

Failed to connect to cibersortx.stanford.edu:80: Connection timed out

1

I have an error that is probably related to proxy settings as the problem disappears when I connect with a private network. I've already set the proxy settings in Rprofile...

kaizen89

EcoTyper does not handle spaces in path names

2

I have a dropbox business account and I'm trying to run EcoTyper example tutorial but I get an error due to the dropbox root folder name containing a space, even...

kaizen89

EcoTyper State Recovery ScRNAseq Error

1

Hello, I've been trying to look at scRNAseq data of carcinomas previously published in Lucas et al. Cell 2021. I've had some trouble with putting through the scRNAseq data of...

dkwon6