Vivian Li Lab

icon indicating a website link vivianli.org

icon company University of California, Riverside icon location Statistical and bioinformatics methods developed by the Wei Vivian Li Lab.

Results 26 comments of Vivian Li Lab

how can I access the HIERARCHICAL structure identified by Louvain clustering?

Hi antonkratz, I wonder if you have found a solution?

how can I access the HIERARCHICAL structure identified by Louvain clustering?

Thanks a lot for the discussion!

Part of the data not imputed

Thank both for the reports. I am looking into this issue and will update you when it's fixed.

Part of the data not imputed

The problem is now fixed in v0.09. Thank you very much for your comments!

outfile is space delimited rather than tab delimited

Hello wangz10, scImpute uses write.table to save the output to txt. The default setting of this function is to generate space delimited files.

About the 'genelen'

Hi, It would be best to calculate gene length based on the same reference version you used to align the reads. I'm not sure if there is such information readily...

error of 'missing value where TRUE/FALSE needed'

Hello xutongran, Can you check if your tumor.tpm file is in the csv format? Does it contain any missing or negative values?

Parallel Processing cannot find library

Hello gouinK, I've never seen this error before, and it's difficult to diagnose the problem with the information you provided. I think you can first check if the penalized package...

No parallel version

Hello, What system and version of R are you using? I am attaching the session information on my end: ``` > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Running...

Differential gene co-expression analysis using scLink

Hello, We didn't try to construct one single network from all gene expression data. Please also note that, in our real data study on the breast cancer, we assessed the...