Pando

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regions parameter in initate_grn()

4

Hi @joschif, The vignette reads that we can constrain the set of candidate regions by providing a GenomiicRanges object in the regions argument. Does Pando package come with phastConsElements20Mammals.UCSC.mm10 or...

sylestiel

Hi, thank you for this useful package! I I ran Pando with my data and I got a SeuratPlus object. Now I would like to explore the regions with high...

valentinaOpazo

Error:infer_grn(),

5

Hi,When I was running this function, I encountered the following error, I checked my motif matrix and gene name, but I did not find a number beginning, I feel very...

wxpbioinfo

input data normalisation

7

Can you clarify what preprocessing is expected for the RNA assay (gene expression) data. Is the expected input integer (raw) counts or normalised&log transformed counts or similar? this isn't totally...

bjstewart1

Advice about a dataset with conditions

4

hi @joschif, congrats on the publication and thank you for porting the analysis in a package! I would like to ask for an advice for analyzing a 10x multiome dataset...

AmelZulji

Error in find_motifs with invalid version slot in SeuratPlus object

5

Hi, I am using Seurat version '4.3.0' and SeuratObject '5.0.1' to run Pando, but I get an error when I run find_motifs: ``` Error in validObject(.Object) : invalid class "SeuratPlus"...

jsacco1

Error in infer_grn()

5

Dear Pndo developers, I was wondering if you could help me to debug my code - I am just following your tutorial and applying it on my data below, however...

TerezaClarence

Question on grn output: how to interpret the grn output where there are list of TFs and their target genes?

1

The column consists of "estimate", "statistic" and "correlation" among others. What do the former mean really? For example, an X-gene is being unregulated at level of mRNA, then the TF...

yojetsharma

Error in as_igraph_vs(graph, from) : Invalid vertex names while running plot_tf_network

1

I am trying to plot the tf network graph. However it gives me that error. Not sure what is happening. ``` > ctrl_multiome ctrl_multiome ctrl_multiome ctrl_multiome ctrl_multiome sessionInfo() R version...

yojetsharma

plot_network_graph() only plot target genes

1

Hi, The dimension of `seurat_object@grn@networks$glm_network@graphs$umap_graph` is the same as number of target genes saved in `seurat_object@grn@networks$glm_network`. As a result, only TFs that are also target genes were plotted. Is this...

zhenzuo2