Yojet

Monocle 3 error: plot_cells(cds, color_cells_by="cao_cell_type") gives the following error:color_cells_by must one of 'cluster', 'partition', 'pseudotime, or a column in the colData table.

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How do I correct the above error? I have loaded the my scRNA data using load_mm_data. Please help. And before that step, I received the following: plot_cells(cds) No trajectory to...

Duplicate cell name error in Cell_Highlight_Plot, even though they are not duplicate

1

Error in `Cell_Highlight_Plot()`: ! The list of `cells_highlight` contains duplicate cell names. ℹ Ensure all cell names are unique before plotting. Run `rlang::last_trace()` to see where the error occurred.

``` Restarting R session... Loading required package: SeuratObject Loading required package: sp Attaching package: ‘SeuratObject’ The following object is masked from ‘package:base’: intersect > library(Seurat) > library(reticulate) > library(dplyr) Attaching...

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

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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...

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...

While everything else ran smoothly, there is an issue while running JASPAR. Also in the script earlier (shown here below): ``` > library(TFBSTools) > library(JASPAR2020) > > pfm df_pfm >...

I am not sure how to go ahead with the analysis. Can someone please help? ``` > pfm df_pfm > seurat open_peaks peaks_matched

I have total of 4-multiome dataset(1-control, 3-patients), which I merge and use it for downstream analysis. Everything is fine until I reach step3 of analysis on the RNA assay. I...

SummarizedExperiment Error with import10xFeatureMatrix function

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``` > ArrowFiles archr / || \\##==......\ / || ______ = =|__ /__ || \\\ ,--' ,----`-,__ ___/' --,-`-===================##========> \ ' ##_______ _____ ,--,__,=##,__ /// , __== ___,-,__,--'#' ===' `-'...

I have my own dataset proceesed using scanpy and another snRNA seq dataset from https://cell.ucsf.edu/snMultiome/ that I plan to use as a reference. From what I understood, I would first...