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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)
https://oncopathtk.org
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Implements sorting by default on most endpoints
#302
jimmymathews
closed
6 months ago
0
Include utility for feature deletion
#301
jimmymathews
closed
6 months ago
0
Utility to delete one feature
#300
jimmymathews
closed
6 months ago
1
Implement cell-level api endpoint
#299
jimmymathews
closed
6 months ago
0
Cell level data
#298
jimmymathews
closed
6 months ago
5
add new specifiers to DataAccessor importance
#297
CarlinLiao
closed
6 months ago
0
Analysis replication DataAccessor is missing new importance score specifiers
#296
CarlinLiao
closed
6 months ago
0
Counts files to db migration
#295
wooferclaw
closed
6 months ago
4
Quick patch to counts_by_signature to handle if one of positive or negative is empty
#294
CarlinLiao
closed
7 months ago
1
`DataAccessor.counts_by_signature` fails if either no positive or no negative markers are provided
#293
CarlinLiao
closed
7 months ago
0
Add support for graph-transformer plugin
#292
CarlinLiao
closed
7 months ago
7
Modularize workflow Nextflow files
#291
CarlinLiao
closed
7 months ago
0
Balance graph datasets
#290
CarlinLiao
opened
7 months ago
0
Modularize graphs workflow
#289
CarlinLiao
closed
7 months ago
0
prevent package caching in Docker images
#288
CarlinLiao
closed
7 months ago
1
Make `spt workflow configure` support both Docker and Singularity
#287
CarlinLiao
closed
7 months ago
20
Expand workflow configure support for singularity
#286
CarlinLiao
closed
7 months ago
1
No option to show Nextflow logs when running the test suite
#285
CarlinLiao
opened
8 months ago
3
Allow saved graphs to be readable without importing spatialprofilingtoolbox
#284
CarlinLiao
closed
8 months ago
1
Convert cggnn/graphs and workflow configure to use config files (redo)
#283
CarlinLiao
closed
8 months ago
17
Dockerize `spt cggnn train` (redo)
#282
CarlinLiao
closed
8 months ago
1
Convert cggnn/graphs and workflow configure to use config files
#281
CarlinLiao
closed
8 months ago
8
Save adjacency matrices separately
#280
CarlinLiao
closed
8 months ago
1
scipy sparse matrix compatibility issues
#279
CarlinLiao
closed
8 months ago
0
Refactor `spt workflow configure` to accept a generic configuration file instead of CLI arguments
#278
CarlinLiao
closed
8 months ago
1
Rename `cg-gnn` submodule to `graphs`
#277
CarlinLiao
closed
9 months ago
4
Dockerize `spt cggnn train`
#276
CarlinLiao
closed
8 months ago
12
Dockerization of the `cg-gnn` model
#275
CarlinLiao
closed
8 months ago
4
Would adding ` --no-cache-dir` to pip install commands slim down Docker image sizes?
#274
CarlinLiao
closed
7 months ago
8
Compartmentalize DGL and torch usage to `histocartography` and `cg_gnn_helper`
#273
CarlinLiao
closed
9 months ago
4
Abstract out graph deep learning functionality to an external plugin system
#272
CarlinLiao
closed
8 months ago
9
Compartmentalize dependency on DGL and torch to cg-gnn model
#271
CarlinLiao
closed
9 months ago
2
replace histocartography with cg-gnn submodule
#270
CarlinLiao
closed
9 months ago
0
Convert `cg-gnn`/`histocartography` to a git submodule
#269
CarlinLiao
closed
9 months ago
6
Add tmi2022 GNN model
#268
CarlinLiao
closed
7 months ago
6
adjust specimen allocation
#267
CarlinLiao
closed
9 months ago
9
Stabilize GNN training/validation/test set creation when given bimodal specimen sizes
#266
CarlinLiao
closed
9 months ago
0
Add urothelial dataset run results
#265
jimmymathews
closed
5 months ago
1
il2 importance analysis
#264
CarlinLiao
closed
9 months ago
5
Add importance score evaluations to analysis_replication
#263
CarlinLiao
closed
9 months ago
0
Add rigorous checks for analysis reproduction
#262
jimmymathews
closed
9 months ago
0
fix cggnn nextflow on small specimens
#261
CarlinLiao
closed
9 months ago
0
cggnn workflow errors if no graphs are created from a specimen
#260
CarlinLiao
closed
9 months ago
5
Moved rest of `cg-gnn` into SPT
#259
CarlinLiao
closed
9 months ago
0
Deprecate database views
#258
jimmymathews
closed
9 months ago
0
Fully move `cg-gnn` pip package into SPT
#257
CarlinLiao
closed
9 months ago
1
Replace cggnn distance matrix with KDTree
#256
CarlinLiao
closed
9 months ago
7
cggnn ROI creation is slow
#255
CarlinLiao
closed
9 months ago
0
Remove unused cg-gnn requirement from pyproject
#254
CarlinLiao
closed
9 months ago
2
Remove dangling requirements for `cg-gnn`
#253
CarlinLiao
closed
9 months ago
0
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