Yichen Wang

icon indicating a website link https://mvfki.github.io/

icon company @welch-lab icon location Ann Arbor icon location Bioinformatician Intermediate @welch-lab , DCMB, UofM // Previously @campbio // MS in Bioinformatics, BU // BS in Life Science, ShanghaiTech University

Results 28 comments of Yichen Wang

no slot name "defaultCluster" for this object of class "liger"

Hi @Obtusah , `defaultCluster` is technically not a "slot" of a `` class object in R terms. You'll be able to access it with getter function `defaultCluster(sr_liger)` once you have...

Proper axis labels 2D Plots

Revisiting Issues now, and you know it's finally fixed in rliger2.

*** caught segfault *** error when running quantile_norm function

We have updated rliger quite a lot in new version 2.0. It seems that the original error message corresponds to a pretty old version so I'm closing this Issue now....

cell type annotation in metadata disappear

Folks I got a dirty fix but works ⬆️

Error when some clusters are not presented in some of the datasets

I did exactly the same. Anyway, I figured out that the real issue is that I should have biological replicates of the same condition as one individual dataset, instead of...

Query on building shared factor neighborhood graph

Hi Yu, I think you're right with point 2. For point 1, briefly, what happens in `quantileNorm()` is that we label cells by the max factor loading (e.g. cluster 1...

fix setting defaultDimRed

Hi Sam, Thank you for being our active user! Indeed I have found this a problem a while ago and have already got a fix in my dev branch. Would...

fix setting defaultDimRed

So basically I got one more step before setting. If the defaultDimRed is set, don't update it by default unless explicitly asked with `asDefault`. If defaultDimRed is NULL, just set...

How to improving similarity between snRNA-seq and snATAC-seq nuclei, by tuning parameters like 'k', 'lambda'?

I've had Josh's recommendation addressed in a way that reference will be automatically chosen from an RNA dataset if the modalities is properly set when creating a liger object, and...

how to deal with batch in cross species comparison?

The first thing you definitely want to do is to convert mouse gene names to their homologous ones in human genes. For example, rename mouse gene "Nkg7" to human homologous...