spateo-release

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We still need to resolve the dependency issues. As of now, there are two significant factors to consider: - [ ] Version upgrade: Version 1.2.0 (commit 1f31391) does not include...

Ukyeon

This push request add the ligand/receptor data to the package and uses package data within functions

1

Firstly, I added a `__init__.py` file in the spateo/tools/database (where the ligand-receptor files are stored) Then I added a MANIFEST.in file, understand the same folder of setup.py, with the following...

Xiaojieqiu

add BasePlot HeatMap classes

Xiaojieqiu

not enough memory to run construct_surface

2

my data contain 580000 cells and I run the construct_surface function and kernal die, any solutions to solve this mem issue . embryo_mesh, _,_ = st.tdr.construct_surface(pc=embryo_pc, key_added="tissue", alpha=0.6, cs_method="marching_cube", cs_args={"mc_scale_factor":...

caiquanyou

Optimized `SCC` Implementation and Removed `TensorFlow` Dependencies

8

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...

Starlitnightly

AttributeError: module 'spateo.pl' has no attribute 'spatial_domains'

1

I did combined visualization of domains and segmented cells using example data, when I run st.pl.spatial_domains(adata_bin30, bin_size=30, label_key="domain_scc_anno") I got this error: AttributeError: module 'spateo.pl' has no attribute 'spatial_domains' ​

Donbbit

Optimized SCC performance & fix some bugs

1

Spatial constrained clustering code in Spateo is very slow now even for small sparse matrix input. The problem is because when use sparse matrix input, the transformation from matrix to...

Purkinje-cell

Remove `trame` and `trame-server` from requirements

1

Sichao25

Sichao25

Clean up the requirement package

2

Clean up the requirement package @chansigit @Sichao25 @YifanLu2000

YifanLu2000