ysuzukilab / cibersortx Goto Github PK

Hello great team,

I am your old user of CIBERSORT. As far as I'm concerned, this great tool experience is awesome. This time I want to try your new tool about CIBERSORTx to get the expression and marker of cell types identified from tissue. Although I login in your website but can not start for running. Is it because the tools are not open yet ? What should I do next?

Best wish!

Yichel

Hi @nina2727,

I'm a new Cibersortx user and I was wondering if you have encountered an error similar to the one I am seeing below:

Error in if (max(m) < 50) { : missing value where TRUE/FALSE needed Calls: CIBERSORTxFractions -> makeRefandClassFiles Execution halted

I am using a single cell counts matrix from our dataset and running the Create Signature Matrix module of Cibersortx. Thanks in advance for your time and help :)

Hi Admin and nina2727,
I have been using Cibersortx since past few days but suddenly it has stopped showing the log and the processed results for any of my jobs and throwing a warning: "The system queue is not running. Please contact the CIBERSORTx Team at [email protected]."

I have contacted their team but haven't heard anything back from them. Do any of you have any idea how can I resolve this issue?

Thanks

Hi @nina2727 ,
I have a data matrix having 20000 genes from 450 samples.
I am new with Cibersortx and have few queries. These may be naive questions:

1. In order to increase the speed for the analysis, is it ok if I divide my samples into two or more smaller groups (like 225 each) and later merge them together.
2. Is there a way with which I can increase the number of threads? (by default it uses 3 threads)

Looking forward to your answers.
Thanks

Hi Team,
CIBERSORTx website suddenly stopped working. I tried with different browser but could not access it. Can you please look into the matter?

Hi all, i am using Cibersotx to deconvolve TCGA gene expression data and getting my the expression values in fractions. I am not sure whether these should be considered as normalized count to perform differential expression among samples or we require any normalization as TMM in EdgeR. Anybody has any experience with this?
Thanks in advance.

@nina2727 would you like to make any suggestion here?

Hi,
I am using cibersortx in the docker, and I am trying to apply my own scRNA-seq matrix. When I run the follow command, I get no files in my output folder, but I get no error when running it neither. What could be happening?

docker run -v "input_directory":/src/data -v "output_directory/output":/src/outdir cibersortx/fractions --myusername --token mytoken --single_cell TRUE --refsample reference_matrix.txt --mixture values_metabric_v1.txt --rmbatchBmode TRUE --perm 100

I did run before cibersortx with docker, but applying the LM22 sigmatrix instead, so it is not problem of the docker or the mixture (which was the same as now). I also try to apply the same command line with one of the examples, and it seems to work because I do get output.
My reference_matrix.txt looks like this (it has more than one cell type even if you can't see it in the picture):

Thank you,
Best,

Paula

Hi,
Recently, Errors always happen (Impute Cell Fractions) as follows, I don’t know how to fix it.

Errors were encountered in CIBERSORTx configuration, run aborted:

Error in mcfork() :
unable to fork, possible reason: Cannot allocate memory
Calls: CIBERSORTxFractions -> CoreAlg -> mclapply -> lapply -> FUN -> mcfork
Execution halted
Warning message:
system call failed: Cannot allocate memory

Job Parameters used for this run:

Date: 2021-02-01 08:00:23
Job type: Impute Cell Fractions
Signature matrix file: CIBERSORTx_Job3_signatures.brain.roc.seurat4.res14.majortype_inferred_phenoclasses.CIBERSORTx_Job3_signatures.brain.roc.seurat4.res14.majortype_inferred_refsample.bm.K999.txt
Mixture file: mixture.brain.roc.majortype.txt
Batch correction: disabled
Disable quantile normalization: true
Run mode (relative or absolute): relative
Permutations: 1

Quan Cheng

We try to use ecotyper in our scRNA-Seq datasets with de novo model in ecotyper.
We need the Token of CIBERSORTx for docker images. And we have asked for the Token from the website.
Could you share us that file?

you might like this:
https://github.com/MaayanLab/clustergrammer

Hi, thanks for this great software!
I have the following question:
Why the estimated proportions for some samples can change if I use a subset of the bulk RNA seq samples, but keeping the same single cell reference and signature matrices?
For instance:

1. First, I used a mixture matrix containing 10 bulk RNA-seq samples (Job12). The proportion of GPM6A neurons for each of the last three samples is aprox 0.7.
2. Then, if I run estimate proportions considering the mixture matrix containing only the last three samples, but the same single cell reference and signature matrices, the estimated proportions are around 0.3 (Job13)

Thanks for your kind help,
Best,
Sofia
CIBERSORTx_Job12_Results.pdf
CIBERSORTx_Job13_Results.pdf

Hi @nina2727,

I am trying to run Cibersortx but every time I get a similar error:
`../lib/cx.sh: line 7: 10746 Killed Rscript $1
or
../lib/cx.sh: line 7: 22543 Killed Rscript $1

`
Is it (10746) a random number or there is some issue with the gene at 10746 row. Can anyone please help, what does this error mean?
I am really stuck. Kindly help.

Thanks

Hi
Is there any way with which I can download the stacked bar chart from Cibersortx?

Thanks