-
As discussed earlier it might be worth investigating the use of [scikit-build](https://github.com/scikit-build/scikit-build) for integration with Cmake, instead of the custom logic currently defined i…
-
Hello @RubD @andrewdchen,
Does Giotto have any option to run normalization across multiple integrated samples (not individually) to minimize background noise and allow reasonable comparisons?
Seu…
-
Hi there,
Firstly - excellent tool! I really like the outputs so far.
I'm trying to map my single cell dataset onto my spatial dataset using RANK enrichment (script below from your website).
…
-
Hello,
Thanks again for this great tool!
While using Giotto, I noticed that while the size of objects are very small (great), the memory usage remains high after running any analysis. I tried to…
-
Hi,
I have a seurat object which I would like to convert into signature matrix. The data is lognormalized and I am using Seurat's `AverageExpression` function to generate the signature matrix. I w…
-
Hi,
I'm trying to create a Giotto object with a pre-computed PCA. When I try to pass a list with the PC matrix, i.e. `dimension_reduction=list("pca"=as.matrix(PCs))`, I receive the following error.…
-
**Submitting author:** @ALuchinsky (Alexey Luchinsky)
**Repository:** https://github.com/ALuchinsky/tdavec
**Branch with paper.md** (empty if default branch):
**Version:** v1.0.0
**Editor:** Pending
…
-
Move to Suggests:
- [x] Rtsne
- [x] plotly
- [x] ggrepel
- [x] limma
Isolate to GiottoVisuals
- [x] cowplot
Move to GiottoUtils
- [x] jsonlite
- [x] progressr
- [x] reshape2
-
Hi Ruben,
When I use the example code of `Giotto`, I met a problem.
Here is my code and error:
````R
mini_visium
-
Running pytest gtda produces two failed tests.
```
FAILED gtda/mapper/tests/test_visualization.py::test_pipeline_cloned[False] - AssertionError
FAILED gtda/mapper/tests/test_visualization.py::tes…
beew updated
4 months ago