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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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Separate datasets for performance and modularity
#230
jimmymathews
closed
1 year ago
0
Reduce CLI command setup time
#229
jimmymathews
closed
1 year ago
1
Implement timeout for ondemand computations
#228
jimmymathews
closed
1 year ago
1
cggnn workflow nextflow configuration
#227
CarlinLiao
closed
1 year ago
19
Slim down expression quantification index
#226
jimmymathews
closed
1 year ago
1
Separate datasets as databases
#225
jimmymathews
closed
1 year ago
0
Make substudy consistent for ondemand computed features.
#224
jimmymathews
closed
1 year ago
0
Restore pending functionality for on-demand metrics
#223
jimmymathews
closed
1 year ago
1
Deprecate resource-intensive views
#222
jimmymathews
closed
12 months ago
1
Replace filesystem intermediate cache files
#221
jimmymathews
closed
9 months ago
1
Work around memory limit problem
#220
jimmymathews
closed
1 year ago
0
Memory limits during application initialization
#219
jimmymathews
closed
1 year ago
5
Null data values conversion to JSON
#218
jimmymathews
closed
1 year ago
1
Visualization WIP
#217
franciscouzo
closed
7 months ago
0
Data type inconsistencies between database, processing, and output
#216
CarlinLiao
closed
1 year ago
2
Add service-specific initialization logic. Waiting etc.
#215
jimmymathews
closed
1 year ago
0
One delegate for initialization phase for ondemand services
#214
jimmymathews
closed
1 year ago
0
Possibly removing the "C" and "P" naming convention in feature columns
#213
jimmymathews
closed
1 year ago
2
Vectorize FME pullers
#212
CarlinLiao
closed
1 year ago
31
Get fraction of important cells expressing phenotype
#211
CarlinLiao
closed
1 year ago
35
small patches
#210
CarlinLiao
closed
1 year ago
1
final step to make cggnn importance scores available in sample-level features
#209
jimmymathews
closed
1 year ago
1
hotfix cggnn scripts, streamline calls
#208
CarlinLiao
closed
1 year ago
13
`make test` distinguish between module and unit tests
#207
CarlinLiao
closed
1 year ago
1
`FeatureMatrixExtractor` should return DataFrames with `bool` values for channels and phenotypes instead of `int`
#206
CarlinLiao
closed
11 months ago
2
`PhenotypeCriteria` should not use `list` data structures
#205
CarlinLiao
closed
1 year ago
1
Upload importance scores via cggnn command
#204
CarlinLiao
closed
1 year ago
3
allow starting only one ondemand service
#203
CarlinLiao
closed
1 year ago
3
Enable specialization of on-demand service for one of the 3 computation types
#202
jimmymathews
closed
1 year ago
0
Bug in squidpy metrics computation, co-occurrence
#201
jimmymathews
closed
1 year ago
3
Bug duplicated identifiers for quantiative_feature_value records
#200
jimmymathews
closed
1 year ago
2
Add replication of analysis scripts
#199
jimmymathews
closed
1 year ago
0
Added security headers library for fastApi
#198
wooferclaw
closed
1 year ago
3
Bug in squidpy metrics computation
#197
jimmymathews
closed
1 year ago
5
Add db managements script to drop pending computatations
#196
jimmymathews
closed
1 year ago
0
Add db management script for dropping pending computations
#195
jimmymathews
closed
1 year ago
0
Analysis replication scripts
#194
jimmymathews
closed
1 year ago
0
Fix slow load of very cacheable items
#193
jimmymathews
closed
1 year ago
0
Slow initial study load due to repeated big count command
#192
jimmymathews
closed
1 year ago
0
Consolidate spatial metrics
#191
jimmymathews
closed
1 year ago
0
Consolidate spatial metrics endpoints
#190
jimmymathews
closed
1 year ago
0
More flexible phenotype arguments for spatial metrics
#189
jimmymathews
closed
1 year ago
0
Argument flexibility for spatial metrics endpoint
#188
jimmymathews
closed
1 year ago
1
Remove support for all-study pulls in `FeatureMatrixExtractor`
#187
CarlinLiao
closed
1 year ago
0
Add study lookup from specimen
#186
jimmymathews
closed
1 year ago
0
create cg-gnn extraction script
#185
CarlinLiao
closed
1 year ago
46
Normalize database config file vs cursor etc
#184
jimmymathews
closed
1 year ago
2
Add squidpy metrics
#183
CarlinLiao
closed
1 year ago
16
`DatabaseConnectionMaker` backward compatibility with `database_config_file`
#182
CarlinLiao
closed
1 year ago
2
Reduce verbosity of some log statements
#181
jimmymathews
closed
1 year ago
0
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