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[![documentation](https://readthedocs.org/projects/spateo-release/badge/?version=latest)](https://spateo-release.readthedocs.io/en/latest/)
[Installation](https://spateo-release.readthedocs.io/en/latest/installation.html) - [Tutorials](https://spateo-release.readthedocs.io/en/latest/tutorials/index.html) - [API](https://spateo-release.readthedocs.io/en/latest/autoapi/spateo/index.html) - [Citation](https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(22)00399-3) - [Technical](https://spateo-release.readthedocs.io/en/latest/technicals/index.html)
# spateo-release
Spatiotemporal modeling of spatial transcriptomics
Cells do not live in a vacuum, but in a milieu defined by cell–cell
communication that can be quantified via recent advances in spatial
transcriptomics. Here we present spateo, a open source framework that
welcomes community contributions for quantitative spatiotemporal
modeling of spatial transcriptomics. Leveraging the ultra-high
spatial-resolution, large field of view and high RNA capture sensitivity
of stereo-seq, spateo enables single cell resolution spatial
transcriptomics via nuclei-staining and RNA signal based cell
segmentation. Spateo also delivers novel methods for spatially
constrained clustering to identify continuous tissue domains, spatial
aware differential analyses to reveal spatial gene expression hotspots
and modules, as well as the intricate ligand-receptor interactions.
Importantly, spateo is equipped with sophisticated methods for building
whole-body 3D models of embryogenesis by leveraging serial profilings of
drosophila embryos across different stages. Spateo thus enables us to
evolve from the reductionism of single cells to the holisticism of
tissues and organs, heralding a paradigm shift in moving toward studying
the ecology of tissue and organ while still offering us the opportunity
to reveal associated molecular mechanisms.
## Spateo Development Process
- Follow feature-staging-main review process
- create a specific branch for new feature
- implement and test on your branch; add unit tests
- create pull request
- discuss with lab members and merge into the main branch once all checks pass
- Follow python [Google code style](https://google.github.io/styleguide/pyguide.html)
## Code quality
- File and function docstrings should be written in [Google style](https://google.github.io/styleguide/pyguide.html)
- We use `black` to automatically format code in a standardized format. To ensure that any code changes are up to standard, use `pre-commit` as such.
```
# Run the following two lines ONCE.
pip install pre-commit
pre-commit install
```
Then, all future commits will call `black` automatically to format the code. Any code that does not follow the standard will cause a check to fail.
## Unit testing
Unit-tests should be written for most functions. To run unit tests, simply run the following.
```
# Install ONCE.
pip install -r dev-requirements.txt
# Run test
make test
```
Any failing tests will cause a check to fail.
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spateo 离线安装包
共174个文件
py:134个
md:8个
csv:5个
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2022-07-29
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空间转录组学的时空建模软件spateo ,通过将dynamo全局调用 改为局部调用,修复导入spateo 自动打开ipython的异常问题,修复空间marker计算函数。软件源来自`https://github.com/aristoteleo/spateo-release`;
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spateo 离线安装包 (174个子文件)
make.bat 766B
setup.cfg 226B
override.css 2KB
sphinx_gallery.css 545B
lr_network_drosophila.csv 815KB
lr_network_mouse.csv 623KB
lr_network_human.csv 512KB
lr_network_zebrafish.csv 321KB
lr_network_axolotl.csv 49KB
.gitignore 718B
.gitmodules 283B
SS200000135TL_D1_bin1_small.gem.gz 394KB
markov_random_field.jpg 17KB
LICENSE 1KB
Makefile 1KB
Makefile 607B
cell_segmentation.md 22KB
README.md 3KB
index.md 3KB
contributing.md 1KB
installation.md 995B
index.md 385B
index.md 299B
contributors.md 71B
tdr.png 1.3MB
cell_segmentation.png 504KB
logo.png 186KB
thin_plate_spline.png 12KB
utils.py 59KB
scatters.py 46KB
three_dims_plots.py 29KB
spagcn_utils.py 25KB
configuration.py 25KB
cell_communication.py 23KB
label.py 22KB
utils.py 21KB
cluster_degs.py 21KB
deep_interpolation.py 19KB
three_dims_plotter.py 18KB
lisa.py 18KB
icell.py 18KB
bgi.py 17KB
three_dims_align.py 17KB
utils.py 16KB
paste.py 15KB
roi.py 15KB
agg.py 14KB
changes.py 13KB
reconstruction_methods.py 12KB
utils.py 11KB
nanostring.py 11KB
mesh_model.py 11KB
em.py 10KB
tree.py 10KB
vi.py 10KB
contour.py 10KB
density.py 10KB
cci_two_cluster.py 10KB
slice.py 9KB
align.py 9KB
find_clusters.py 9KB
utils.py 9KB
model_utils.py 9KB
test_icell.py 9KB
borderline.py 8KB
grid.py 8KB
conf.py 8KB
coarse_align.py 8KB
stardist.py 8KB
interpolation_nn.py 8KB
architype.py 7KB
space.py 7KB
interpolations.py 7KB
pick.py 7KB
benchmark.py 7KB
qc.py 7KB
bbs.py 7KB
filter.py 6KB
agg.py 6KB
bbs.py 6KB
moran.py 6KB
geo.py 6KB
contour.py 6KB
get_version.py 6KB
simulation.py 6KB
mesh_utils.py 6KB
utils.py 6KB
cluster_spagcn.py 5KB
clip.py 5KB
bp.py 5KB
vtk_interpolate.py 5KB
test_utils.py 5KB
test_label.py 5KB
slideseq.py 4KB
morphology.py 4KB
test_em.py 4KB
label_utils.py 4KB
spatial_degs.py 4KB
colorlabel.py 4KB
cluster_lasso.py 4KB
共 174 条
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