Zehua Zeng
Zehua Zeng
Hi I'm interested in utilizing this pipeline in CHM13 reference. How can I make a new reference gene file from 'gtf' or other file ?? All the best Sincerely Zehua
add file 'annotations/T2TCHM13_refgenes.txt' add argument 'T2TCHM13' for scatac-genescore in file 'scATAC_Genescore.py' Since I used the T2TCHM13 reference genome for the scATAC-seq comparison, after comparing the difference between GRCh38 and T2TCHM13,...
When installing `spateo` on macOS, I encountered version incompatibility errors. For instance, the `vtk` package requires a minimum Python version of 3.9. Additionally, installing both `torch` and `tensorflow` simultaneously can...
### systemRole Below is a paragraph from an academic paper. Polish the writing to meet the academic style, improve the spelling, grammar, clarity, concision and overall readability. When necessary, rewrite...
In version 1.6.5: - [ ] Added [spectra](https://github.com/dpeerlab/spectra) to calculate the score of geneset - [x] Added [Starfysh](https://www.nature.com/articles/s41587-024-02173-8#Abs1) to integrates spatial transcriptomic and histologic data - [x] Added dotplot using...
## Pull Request Information The error in `scMulan` encountering is due to attempting to find the maximum value in an empty array, which results in a ValueError. To handle this...
The new tutorial could be found in https://dynamo-release-test.readthedocs.io/en/latest/index.html. 1. It is important to note that the notebook for this tutorial depends on [dynamo-tutorials](https://github.com/aristoteleo/dynamo-tutorials/), but there are some issues related to...
- [x] Add the adjustText package to solve the issue of legend overlap. - [x] Optimize the display of the tutorial page. - [x] Reproduce all the tutorials and optimize...
# Conventional scRNA-seq - [x] notebooks/zebrafish - [x] notebooks/zebrafish_topography_analysis_tutorial # Differential geometry - [x] notebooks/tutorial_hsc_dynamo_megakaryocytes_appearance - [x] notebooks/tutorial_hsc_dynamo_cellwise_analysis - [x] notebooks/tutorial_hsc_dynamo_basophil_lineage - [x] notebooks/Differential_geometry # Labeling scRNA-seq - [x] notebooks/scNT_seq_readthedocs...
If you have any feature requests, you can reply within this issue or create a new issue. - [ ] Added `CellVote` to annotate the cell type automatically - [...