pakiessling
pakiessling
Hi I am on scanpy=1.9.3 squidpy=1.2.3 tangram=1.0.4 torch=1.13.1+cu117 I am trying to integrate single cell and merfish data. A marker list of 104 genes was correctly prepared and I have...
### Description of feature Hi, unsure if this is supported yet. 10x offers new kits to process scRNA from FFPE https://www.10xgenomics.com/products/single-cell-gene-expression-flex The data is processed with `cellranger multi` https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi It...
Hi there, I am working on creating a converter from Baysor output and I notice that a small percentage of Baysor .geojson output contains less than 4 coordinates and is...
Hi, 10x has a newish product ["flex"](https://www.10xgenomics.com/products/single-cell-gene-expression-flex) that allows for the sequencing of fixed nuclei. It works based on [a set of 20 000 probes that bind transcripts](https://www.10xgenomics.com/support/single-cell-gene-expression-flex/documentation/steps/probe-sets/chromium-frp-probe-sets-overview) and are...
`SeuratDisk_0.0.0.9019 SeuratData_0.2.2 sp_1.5-0 SeuratObject_4.1.0 Seurat_4.1.1 ` I convert a rds to h5seurat and then h5ad. I encountered the same problem on multiple datasets. Before: ![grafik](https://user-images.githubusercontent.com/104848590/214296055-38b7f30a-6f20-4396-8357-b8ca5ab349ac.png) After: ![grafik](https://user-images.githubusercontent.com/104848590/214296168-5d48b762-441f-4a7b-8d79-1ca7390891b8.png) The annotation column...
Hi, If you select multiple different regions on a Merscope you get multiple different folders as output. I am trying to combine them into a single object like this: ```...
Hi, thank you for the nice tool. I was wondering how I could apply this tool to my research. I have scRNA samples of different donors. For every donor cells...
3D support
Thank you for the tool, I am interested in trying it out. Is it possible to run the algorithm on 3D data such as the 7 z-levels a Merscope outputs?...
Hi, thank you for this tool, I am very excited to try it out. Unfortunately, my Slideshow is permanently stuck at 404: Not found. Server log says: ``` 404 GET...
Hi, I want to load VisiumHD data in a pipeline without any images, is there a way to accomplish this?