Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nadeemlab/spt issues and pull requests

#274 - Would adding ` --no-cache-dir` to pip install commands slim down Docker image sizes?

Issue - State: closed - Opened by CarlinLiao 12 months ago - 8 comments
Labels: enhancement

#273 - Compartmentalize DGL and torch usage to `histocartography` and `cg_gnn_helper`

Pull Request - State: closed - Opened by CarlinLiao 12 months ago - 4 comments
Labels: refactor

#272 - Abstract out graph deep learning functionality to an external plugin system

Issue - State: closed - Opened by CarlinLiao 12 months ago - 9 comments
Labels: refactor

#271 - Compartmentalize dependency on DGL and torch to cg-gnn model

Issue - State: closed - Opened by CarlinLiao 12 months ago - 2 comments
Labels: refactor

#270 - replace histocartography with cg-gnn submodule

Pull Request - State: closed - Opened by CarlinLiao 12 months ago

#269 - Convert `cg-gnn`/`histocartography` to a git submodule

Issue - State: closed - Opened by CarlinLiao 12 months ago - 6 comments
Labels: enhancement

#268 - Add tmi2022 GNN model

Issue - State: closed - Opened by CarlinLiao 12 months ago - 6 comments
Labels: enhancement

#267 - adjust specimen allocation

Pull Request - State: closed - Opened by CarlinLiao 12 months ago - 9 comments
Labels: enhancement

#265 - Add urothelial dataset run results

Issue - State: closed - Opened by jimmymathews 12 months ago - 1 comment

#264 - il2 importance analysis

Pull Request - State: closed - Opened by CarlinLiao 12 months ago - 5 comments
Labels: enhancement

#263 - Add importance score evaluations to analysis_replication

Issue - State: closed - Opened by CarlinLiao 12 months ago
Labels: enhancement

#262 - Add rigorous checks for analysis reproduction

Pull Request - State: closed - Opened by jimmymathews 12 months ago

#261 - fix cggnn nextflow on small specimens

Pull Request - State: closed - Opened by CarlinLiao 12 months ago
Labels: bug

#261 - fix cggnn nextflow on small specimens

Pull Request - State: closed - Opened by CarlinLiao 12 months ago
Labels: bug

#260 - cggnn workflow errors if no graphs are created from a specimen

Issue - State: closed - Opened by CarlinLiao 12 months ago - 5 comments
Labels: bug

#260 - cggnn workflow errors if no graphs are created from a specimen

Issue - State: closed - Opened by CarlinLiao 12 months ago - 5 comments
Labels: bug

#259 - Moved rest of `cg-gnn` into SPT

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago
Labels: refactor

#259 - Moved rest of `cg-gnn` into SPT

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago
Labels: refactor

#258 - Deprecate database views

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#257 - Fully move `cg-gnn` pip package into SPT

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 1 comment
Labels: enhancement

#257 - Fully move `cg-gnn` pip package into SPT

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 1 comment
Labels: enhancement

#256 - Replace cggnn distance matrix with KDTree

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 7 comments
Labels: enhancement

#255 - cggnn ROI creation is slow

Issue - State: closed - Opened by CarlinLiao about 1 year ago
Labels: enhancement

#254 - Remove unused cg-gnn requirement from pyproject

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 2 comments

#254 - Remove unused cg-gnn requirement from pyproject

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 2 comments

#253 - Remove dangling requirements for `cg-gnn`

Issue - State: closed - Opened by CarlinLiao about 1 year ago
Labels: bug

#253 - Remove dangling requirements for `cg-gnn`

Issue - State: closed - Opened by CarlinLiao about 1 year ago
Labels: bug

#252 - Fix counts provided for specimens without cells in the selected cell list

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago
Labels: bug

#252 - Fix counts provided for specimens without cells in the selected cell list

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago
Labels: bug

#250 - Increase detail of analysis reproduction scripts

Issue - State: closed - Opened by jimmymathews about 1 year ago
Labels: documentation, refactor

#250 - Increase detail of analysis reproduction scripts

Issue - State: closed - Opened by jimmymathews about 1 year ago
Labels: documentation, refactor

#249 - Squidpy null bug

Pull Request - State: closed - Opened by jimmymathews about 1 year ago - 1 comment

#249 - Squidpy null bug

Pull Request - State: closed - Opened by jimmymathews about 1 year ago - 1 comment

#248 - Parallelize `cggnn` workflow

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 7 comments
Labels: refactor

#248 - Parallelize `cggnn` workflow

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 7 comments
Labels: refactor

#247 - Refactor `workflow` module to better match current SPT standards

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 2 comments
Labels: refactor

#246 - Slim down big table indexing

Pull Request - State: closed - Opened by jimmymathews about 1 year ago - 1 comment

#246 - Slim down big table indexing

Pull Request - State: closed - Opened by jimmymathews about 1 year ago - 1 comment

#245 - Update study dropping functionality and add some error guards

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#244 - Add cg-gnn graph generation and plotting

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 7 comments
Labels: feature

#244 - Add cg-gnn graph generation and plotting

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 7 comments
Labels: feature

#243 - FeatureMatrixExtractor channel mismatch in live

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 19 comments
Labels: bug

#243 - FeatureMatrixExtractor channel mismatch in live

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 19 comments
Labels: bug

#242 - Deal with NF string processing for cggnn

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#242 - Deal with NF string processing for cggnn

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#241 - cggnn workflow Nextflow file fails to handle target names with spaces

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 15 comments
Labels: bug

#241 - cggnn workflow Nextflow file fails to handle target names with spaces

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 15 comments
Labels: bug

#240 - Review API endpoints for opportunity to regularize return values (e.g. by sorting)

Issue - State: open - Opened by jimmymathews about 1 year ago - 1 comment
Labels: enhancement

#240 - Review API endpoints for opportunity to regularize return values (e.g. by sorting)

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: enhancement

#239 - Bring data transformation features from `cg-gnn` to SPT

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 9 comments
Labels: enhancement

#238 - handle json-incompliant floats from OnDemandProvider

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 1 comment
Labels: enhancement

#238 - handle json-incompliant floats from OnDemandProvider

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 1 comment
Labels: enhancement

#237 - Implement timeout for ondemand computations

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#236 - Reduce startup time for CLI scripts

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#236 - Reduce startup time for CLI scripts

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#235 - Bug fix to some db management

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#235 - Bug fix to some db management

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#234 - Database name

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: bug

#234 - Database name

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: bug

#233 - Update to support cg-gnn 0.2.1

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 13 comments
Labels: enhancement

#233 - Update to support cg-gnn 0.2.1

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 13 comments
Labels: enhancement

#232 - Supporting `cg-gnn` version 0.2

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 4 comments
Labels: enhancement

#232 - Supporting `cg-gnn` version 0.2

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 4 comments
Labels: enhancement

#231 - Test harness simplification

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: development

#231 - Test harness simplification

Issue - State: open - Opened by jimmymathews about 1 year ago
Labels: development

#230 - Separate datasets for performance and modularity

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#230 - Separate datasets for performance and modularity

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#229 - Reduce CLI command setup time

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: bug

#229 - Reduce CLI command setup time

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: bug

#228 - Implement timeout for ondemand computations

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: bug, enhancement

#228 - Implement timeout for ondemand computations

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: bug, enhancement

#227 - cggnn workflow nextflow configuration

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 19 comments
Labels: feature

#227 - cggnn workflow nextflow configuration

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 19 comments
Labels: feature

#226 - Slim down expression quantification index

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: enhancement

#226 - Slim down expression quantification index

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: enhancement

#225 - Separate datasets as databases

Issue - State: closed - Opened by jimmymathews about 1 year ago
Labels: enhancement

#225 - Separate datasets as databases

Issue - State: closed - Opened by jimmymathews about 1 year ago
Labels: enhancement

#224 - Make substudy consistent for ondemand computed features.

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#224 - Make substudy consistent for ondemand computed features.

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#223 - Restore pending functionality for on-demand metrics

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: bug

#223 - Restore pending functionality for on-demand metrics

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: bug

#222 - Deprecate resource-intensive views

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: enhancement

#222 - Deprecate resource-intensive views

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: enhancement

#221 - Replace filesystem intermediate cache files

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: feature, refactor

#221 - Replace filesystem intermediate cache files

Issue - State: open - Opened by jimmymathews about 1 year ago - 1 comment
Labels: feature, refactor

#220 - Work around memory limit problem

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#220 - Work around memory limit problem

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#219 - Memory limits during application initialization

Issue - State: closed - Opened by jimmymathews about 1 year ago - 5 comments
Labels: bug, enhancement

#219 - Memory limits during application initialization

Issue - State: closed - Opened by jimmymathews about 1 year ago - 5 comments
Labels: bug, enhancement

#218 - Null data values conversion to JSON

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: bug

#218 - Null data values conversion to JSON

Issue - State: closed - Opened by jimmymathews about 1 year ago - 1 comment
Labels: bug

#217 - Visualization WIP

Pull Request - State: closed - Opened by franciscouzo about 1 year ago

#216 - Data type inconsistencies between database, processing, and output

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 2 comments
Labels: refactor, wontimplement

#216 - Data type inconsistencies between database, processing, and output

Issue - State: closed - Opened by CarlinLiao about 1 year ago - 2 comments
Labels: refactor, wontimplement

#215 - Add service-specific initialization logic. Waiting etc.

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#215 - Add service-specific initialization logic. Waiting etc.

Pull Request - State: closed - Opened by jimmymathews about 1 year ago

#214 - One delegate for initialization phase for ondemand services

Issue - State: closed - Opened by jimmymathews about 1 year ago
Labels: bug