Pedram Torabian

Visualization-deconvolved cell types

5

I attempted to visualize some of the results but when I apply the commands, I cannot see the deconvolved cell types properly or distinctly. Also, I should mention that: 1-...

Issue in predict_ligand_activities function

1

I followed this workflow so far: `organism

About introducing the data to Squidpy

3

... To begin with, how we should introduce the data to start the analysis? In the tutorial, it's mentioned that loading data is like this: ```python img = sq.datasets.visium_hne_image() adata...

Pvalue Threshold Error

3

I want to put a threshold for CFDB results. For example greater and/or equal to 0.05. What's the command: Is sth like this: ellphonedb method statistical_analysis meta_subtype2new.txt counts_subtype2new.txt --counts-data=hgnc_symbol --pvalue>0.05...

ExperimentHub with zero records

6

Hi I am trying to use SingleR for annotating my clusters. I would use "Pancreas" datasets but I get this error: "> query(eh, "BaronPancreasData('human')") ExperimentHub with 0 records snapshotDate(): 2022-10-31"...

How to access an image (slice) of interest in spatial analysis

1

Hello I am doing an analysis via fgsea package and when I want to visualize the results, although I have three images (slices) stored in seurat object, I cannot access...

Installing error on Mac

10

Hello. I have a problem to install the 'ensembldb' package on my R studio, based on my Mac M1. However, I get several errors. Error: "cram/cram_io.c:61:10: fatal error: 'lzma.h' file...