Shaowen Jiang comments

Results 19 comments of


                                            Shaowen Jiang

TCGA CNV data without sample type options?

Hi again, sorry for arising another kind of question under this issue. But when I look for the downloaded MAF mutation data from mutect pipeline, I cannot find any fusion...

Questions about the results of pySCENIC

I have just another question might be interesting, So after calculating the RSS, we get a list of rank regulons for each of the clusters. Would it be interested to...

SCTransform Normalize Sequencing Depth

And one more question if you don't mind, What's the difference between "ScaleData(obj, vars.to.regress = "nCount_RNA") Thanks!

Error when saving H5Seurat

Same error here.... Creating h5Seurat file for version 3.1.5.9900 Adding counts for RNA Adding data for RNA No variable features found for RNA No feature-level metadata found for RNA Adding...

add_annotation_col based on cluster or state

Same to me too.

Determining spatial.factors for CurioSeeker platform in creating a CellChat object

Hi @sqjin , why the conversion.factor = 0.73? based on the Slide-seq paper and its method, isn't the conversion factor is 1.54?

Determining spatial.factors for CurioSeeker platform in creating a CellChat object

Hi @sqjin ,for From the original Slide-seq v2 paper github https://github.com/rstickels/Slide_seqv2/blob/master/SlideseqV2_visium_comparison_submission.ipynb In the 18th chunk, they have a conversion factor between the pixel and micrometer, which I guess would be...

Determining spatial.factors for CurioSeeker platform in creating a CellChat object

Also, I am very unsure about how should we set up the scale.distance for the slide-seq data? in the computeCommunProb function? Sorry for bringing this up in this question.

Issues about using salmon quant on multiple bam files

It doesn’t have a problem with a single bam file. Which is the reason make me wonder maybe my command is wrong. Sure, I can share some of the bam...