Cathal King

analysing row-col data from cell profiler

3

I have a question regarding iSEE that I hope that you can help me with. Cell profiler (imaging software) outputs several huge datasets (row-column data frames) which take my wet...

Is there any Seurat objects in the SeuratData package that are compatible with the new v5 Seurat?

```run_numbat()``` error unclear

5

I am trying to use the ```run_numbat()``` function and am running into an error: ``` Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method...

singularity - Error in value

4

I successfully pulled the numbat container with singularity instead of Docker (our HPC only has singularity) with the following: ```singularity pull docker://pkharchenkolab/numbat-rbase:main``` That created a .sif file which contains all...

Is it possible for Monocle to assign cell types on its own? I am working with a dataset that is from Mouse colon that I have processed within a Seurat...

spatial proteomics data to SPE

1

Hi. I have data from a spatial proteomics experiment in the format shown below, which just contains x-y co-ordinates, intensity and mz values. I would like to read this into...

upload multiple Visium samples to the spatialLIBD shiny app

4

Maybe this is already possible? But I have 6 10x Visium datasets that I would like to upload to 1 shiny app for data mining and sharing. If possible, would...

samtools ```split``` on a select list of tags

1

#### Is your feature request related to a problem? Please specify. I would like to split my BAM file based on specific flag in each entry. The input is a...

BD data

4

@rob-p @robsyme @DongzeHE I have BD (Becton Dickinson) single-cell RNA-seq data that I want to align. Can I do this with `simpleaf`? Thanks

iSEE for a SpatialExperiment

2

Can iSEE support Spatial transcriptomics data that is contained within a SPE (SpatialExperiment) object? I have 10x Visium data in an SPE and tried running ```iSEE(SPE)``` which opened a shiny...