Aurora

# If I change "heatmap" to "coverage", then it is giving error. Otherwise Heatmap is fine. l

run RCTD for combined visium data

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Hi, I have just started exploring RCTD. I have two 10x spatial visium slides from brain area. Each slide with 4 sections. So, total 8 samples. These are merged in...

While compiling, I got following error: gcc -Wall -O2 prog.c -o prog -L /usr/local/bin -lfml -lz -lm -lpthread cc1: fatal error: prog.c: No such file or directory gcc (GCC) 12.2.1...

unable to download file, HTTP status was '403 Forbidden'

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counts

generating VCF for REGION_VCF from RNA-seq data

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Hi, This is more naive question as I do not have experience in SNPs. I have 2 cell-lines scRNAseq data, combined sequenced. Now would like to separate using cellSNP (&...

cellchat version 1.6.1 or Version 2.1.2 mouse database plotGeneExpression(cellchat, signaling = "MK", type = "violin") Error in `levels

It installed successfully: pip3 install PyVCF Then we import vcf module in python (removing and reinstalling did not solve the problem): python3 Python 3.7.7 (default, Mar 13 2020, 21:39:43) [GCC...

use of Seurat object

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Hi, can I use Seurat object (with UMAP/clustering already done) just to do the trajectory analysis ? thanks

Hi, I am using pycisTopic. My multiome data was processed in seurat/signac. I added seurat_clusters seurat/signac as metadata column. cell_data = pd.read_csv(projDir+'metadata.txt', sep='\t') cell_data.set_index('cell', inplace=True) cistopic_obj.add_cell_data(cell_data) Then I also added...