psupertime
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wmacnair
psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels
Hi, I've tested with the supplementary dataset from the package "psupplementary". And I met an error as the below. > go_list = psupertime_go_analysis(psuper_obj, org_mapping='org.Hs.eg.db') clustering genes calculating GO enrichments for...
Hi, May I ask how to make predictions for the new independent data? I think it should be: _score = t(new_data_x) %*% psuper_obj$beta_dt$beta_ And they compare the score with _psuper_obj$cuts_dt_...
Thanks for the great package. It really fills a gap in pseudo time analysis. I had a question. Are gene names in which a hyphen got replaced with a dot...
Hi, I have successfully run psupertime on multiple datasets, but I met a weird error for a new dataset: ``` cross-validation training, 5 folds: fold 1 Error in lognet(xd, is.sparse,...
Hi, I've run into this error when installing psupertime with build_vignettes=TRUE: ─ installing the package to build vignettes E creating vignettes (18.3s) --- re-building ‘psuper_intro.Rmd’ using rmarkdown Quitting from lines...
Hi, Thank you for this package. I am trying to fit psupertime model for bulkRNAseq data. I have 40 samples and I am trying to fit the model with donor...
Dear developer, Thank you very much for this nice tool! I was wondering after I have performed psupertime is there a way to display the expression of certain genes along...
from R 4.0.0 onwards, we need to use ```inherits(matrix_obj, "matrix")``` to check that `x` is a matrix, instead of ```class(matrix_obj) == "matrix"```
I successfully installed peupertime with “build_vignettes=TRUE”. When I run the code browseVignettes(package = 'psupertime') in R studio, though I can view “Brief introduction to psupertime - [HTML](http://121.192.179.196:8787/library/psupertime/doc/psuper_intro.html) [source](http://121.192.179.196:8787/library/psupertime/doc/psuper_intro.Rmd) [R code](http://121.192.179.196:8787/library/psupertime/doc/psuper_intro.R)”...
Hi, Thank you very much for this nice and useful package. I am trying to run this on my own data and encountered this error. Please see the codes and...