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nadeemlab
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SPT
Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images
https://oncopathtk.org
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Save adjacency matrices separately
#280
CarlinLiao
closed
11 months ago
1
scipy sparse matrix compatibility issues
#279
CarlinLiao
closed
11 months ago
0
Refactor `spt workflow configure` to accept a generic configuration file instead of CLI arguments
#278
CarlinLiao
closed
10 months ago
1
Rename `cg-gnn` submodule to `graphs`
#277
CarlinLiao
closed
11 months ago
4
Dockerize `spt cggnn train`
#276
CarlinLiao
closed
10 months ago
12
Dockerization of the `cg-gnn` model
#275
CarlinLiao
closed
10 months ago
4
Would adding ` --no-cache-dir` to pip install commands slim down Docker image sizes?
#274
CarlinLiao
closed
10 months ago
8
Compartmentalize DGL and torch usage to `histocartography` and `cg_gnn_helper`
#273
CarlinLiao
closed
11 months ago
4
Abstract out graph deep learning functionality to an external plugin system
#272
CarlinLiao
closed
10 months ago
9
Compartmentalize dependency on DGL and torch to cg-gnn model
#271
CarlinLiao
closed
11 months ago
2
replace histocartography with cg-gnn submodule
#270
CarlinLiao
closed
11 months ago
0
Convert `cg-gnn`/`histocartography` to a git submodule
#269
CarlinLiao
closed
11 months ago
6
Add tmi2022 GNN model
#268
CarlinLiao
closed
9 months ago
6
adjust specimen allocation
#267
CarlinLiao
closed
11 months ago
9
Stabilize GNN training/validation/test set creation when given bimodal specimen sizes
#266
CarlinLiao
closed
11 months ago
0
Add urothelial dataset run results
#265
jimmymathews
closed
8 months ago
1
il2 importance analysis
#264
CarlinLiao
closed
11 months ago
5
Add importance score evaluations to analysis_replication
#263
CarlinLiao
closed
11 months ago
0
Add rigorous checks for analysis reproduction
#262
jimmymathews
closed
11 months ago
0
fix cggnn nextflow on small specimens
#261
CarlinLiao
closed
11 months ago
0
cggnn workflow errors if no graphs are created from a specimen
#260
CarlinLiao
closed
11 months ago
5
Moved rest of `cg-gnn` into SPT
#259
CarlinLiao
closed
12 months ago
0
Deprecate database views
#258
jimmymathews
closed
12 months ago
0
Fully move `cg-gnn` pip package into SPT
#257
CarlinLiao
closed
12 months ago
1
Replace cggnn distance matrix with KDTree
#256
CarlinLiao
closed
12 months ago
7
cggnn ROI creation is slow
#255
CarlinLiao
closed
12 months ago
0
Remove unused cg-gnn requirement from pyproject
#254
CarlinLiao
closed
1 year ago
2
Remove dangling requirements for `cg-gnn`
#253
CarlinLiao
closed
1 year ago
0
Fix counts provided for specimens without cells in the selected cell list
#252
CarlinLiao
closed
1 year ago
0
`OnDemandRequester.get_counts_by_specimen` doesn't error if none of the cells selected are in a specimen it looks at
#251
CarlinLiao
closed
1 year ago
0
Increase detail of analysis reproduction scripts
#250
jimmymathews
closed
11 months ago
0
Squidpy null bug
#249
jimmymathews
closed
1 year ago
1
Parallelize `cggnn` workflow
#248
CarlinLiao
closed
1 year ago
7
Refactor `workflow` module to better match current SPT standards
#247
CarlinLiao
closed
11 months ago
2
Slim down big table indexing
#246
jimmymathews
closed
1 year ago
1
Update study dropping functionality and add some error guards
#245
jimmymathews
closed
1 year ago
0
Add cg-gnn graph generation and plotting
#244
CarlinLiao
closed
1 year ago
7
FeatureMatrixExtractor channel mismatch in live
#243
CarlinLiao
closed
1 year ago
19
Deal with NF string processing for cggnn
#242
jimmymathews
closed
1 year ago
0
cggnn workflow Nextflow file fails to handle target names with spaces
#241
CarlinLiao
closed
1 year ago
15
Review API endpoints for opportunity to regularize return values (e.g. by sorting)
#240
jimmymathews
closed
8 months ago
1
Bring data transformation features from `cg-gnn` to SPT
#239
CarlinLiao
closed
1 year ago
9
handle json-incompliant floats from OnDemandProvider
#238
CarlinLiao
closed
1 year ago
1
Implement timeout for ondemand computations
#237
jimmymathews
closed
1 year ago
0
Reduce startup time for CLI scripts
#236
jimmymathews
closed
1 year ago
0
Bug fix to some db management
#235
jimmymathews
closed
1 year ago
0
Database name
#234
jimmymathews
closed
1 year ago
1
Update to support cg-gnn 0.2.1
#233
CarlinLiao
closed
1 year ago
13
Supporting `cg-gnn` version 0.2
#232
CarlinLiao
closed
1 year ago
4
Test harness simplification
#231
jimmymathews
closed
2 months ago
1
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