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califano-lab / PISCES

R package for Protein activity analysis of single-cell RNAseq.
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Why aren't these two functions (CorDist, LouvainKRange) in the latest package? #16

Open baoyulinn opened 2 years ago

baoyulinn commented 2 years ago

I wanted to use these two functions, but there was none. I want to know how to solve this problem, thank you.

sce.combined.sct <- CorDist(sce.combined.sct, pca.feats = 10)
sce.combined.sct <- LouvainKRange(sce.combined.sct, kmax = 100)
ERIGR commented 2 years ago

Hi, I have the same issue. Could you specify from which packages are coming these two functions please ? Thanks a lot. I'm very interested by PISCES that seems very interesting.

baoyulinn commented 2 years ago

Hi, I have the same issue. Could you specify from which packages are coming these two functions please ? Thanks a lot. I'm very interested by PISCES that seems very interesting.

maybe the older version of this package (devtools::install_github("califano-lab/PISCES"))

ERIGR commented 2 years ago

How did you install the older version ?

baoyulinn commented 2 years ago

How did you install the older version ?

I have not used this package, because i met some error that i could not solve. so i created the ARACNe networks by using other methods.

lvlahos343 commented 2 years ago

You can find these functions in the new version of the package with new names: cor_dist and louvain_k

Previous versions attempted to be compatible with Seurat objects. That's a paradigm we've moved away from for the moment, thought it's something we hope to revisit in the near future. For now, the naming convention has shifted to lower case function names. If we do re-incorporate compatibility with Seurat objects in the future, those will have upper case function names as a way to differentiate the two ways of running the analysis.

ERIGR commented 2 years ago

Thanks, what is the equivalent of pca.feats = 10 in cor_dist ?

ERIGR commented 2 years ago

so the main argument is no more a Seurat matrix but only the scale count matrix I guess ?

ERIGR commented 2 years ago

Do you think you will have a new version associated to new vignette and manual quickly or it will take some times before a complete new release. Just to know if it is smarter to wait or if I should continue to work with the present version. Thanks.