-
I have loaded some data into an SE object using the following code
```
samples
-
Hi @drbecavin,
I am an active contributor to the [nf-core](https://nf-co.re/) project and have been working on the [scRNA-seq](https://github.com/nf-core/scrnaseq) and [spatialtranscriptomics](htt…
-
running code
```
echo `date` "=> image processing and registration start......."
export HDF5_USE_FILE_LOCKING=FALSE
dataDir='/xskydata/project/spatialTranscriptomics/2024/Q3/spat…
-
While I in the end was able to concatenate the data the way I like, the user experience wasn't as great as I had hoped, so wanted to drop some feedback. As I'm not that familiar with spatialdata yet, …
-
### Description of feature
Having individual QC reports for each sample is nice, but it would be cool to have one aggregated report that gives an overview of all samples to quickly identify problemat…
grst updated
2 months ago
-
I'm running part two of the SAW pipeline using manual registration. The first part goes through fine, but when I run the second part I receive the following output and it fails.
```
[WARN 20240219-1…
-
Thank you for developing SPATA! I just started using it to explore some Visium V1 data, and encountered an error in infercnv:::plot_cnv. I used initiateSpataObject_10X to perform the initial analysis …
-
### Description of the bug
Running the nf-core/spatialtranscriptomics pipeline on an EC2 instance with files in S3. Encountered an error in `NFCORE_SPATIALTRANSCRIPTOMICS:ST:ST_DOWNSTREAM:ST_SPATIAL_…
-
### Description of bug
When running with the new Space Ranger MultiQC module I'm getting an error, but not for all input types: it works for Visium chemistry v2, but not v1. I'm guessing that there i…
-
Hi, when I run spatialTIME, there is a error "can't interpret w as a window"; I try to load "maptools" to solve the problem, which didnt work.
If you could help me, much appreciation