STUtility

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@jbergenstrahle @ludvigla @davidecrs Hello STUtility team, I try to install STUtility package in R studio/ R 4.3.2 and I am getting the following > devtools::install_github( + "jbergenstrahle/STUtility", dependencies = TRUE...

krigia

The IntegrateData command from base Seurat deletes the `tools/Staffli` subobject which contains the Spatial Data that STUtility is storing. This normally would not be a problem as it is useless...

corecontingency

neighborhood analysis error

3

Hi, I am hitting an error code when I run neighborhood analysis: > FeatureOverlay(se_EWS4064_normalized, features = "nbs_2", ncols = 2, sampleids = 1:2, cols = c("red", "lightgray"), pt.size = 2)...

chrkuo

Dear STUtility team. When I plot the feature plots using Seurat, and STUtility package. I got two following images that is flipped. can I flip my STUtility derived feature plot...

oghzzang

Enrichment plot function in STUtility

2

Hello @jbergenstrahle @ludvigla @davidecrs Does STutility have any option/function to generate enrichment spatial plots and UMAPs for Visium data? Similar to those generated by another pipeline for spatial analysis: Thank...

krigia

Hi, Thank you for generating this great package, I am using FeatureOverlay(object, spot.colors = color_column) where color_column is a dataframe with the same spot ids as rownames and only one...

behrouzsh

Upload package to conda

1

Thanks for this useful package! I was wondering if you are planning to upload STUtility to conda any time soon.

mj-jimenez

Loupe Browser label transfer go wrong

1

I have a question regarding the differences between the common seurat object image storage and Staffli one. Once I export the .csv file from Loupe Browser, I upload it to...

lsudupe

Issue with Graphics API in ManualAnnotation function

1

Hi! I wanted to ask if there is anyone who is able to help me with this issue that comes up when I try to view my spatial images using...

rebecca-ong

Plot multiple celltypes or genes in a single slice

2

Hi, I am trying to plot expression of multiple genes or probability of multiple celltypes in a single slice, as provided by celllocation.  Any suggestions if we want to...

quanc1989