nadeemlab/spt issues and pull requests

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

Pull Request - State: closed - Opened by CarlinLiao 10 months ago
Labels: refactor

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

Pull Request - State: closed - Opened by CarlinLiao 10 months ago
Labels: refactor

#258 - Deprecate database views

Pull Request - State: closed - Opened by jimmymathews 10 months ago

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

Issue - State: closed - Opened by CarlinLiao 10 months ago - 1 comment
Labels: enhancement

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

Issue - State: closed - Opened by CarlinLiao 10 months ago - 1 comment
Labels: enhancement

#256 - Replace cggnn distance matrix with KDTree

Pull Request - State: closed - Opened by CarlinLiao 10 months ago - 7 comments
Labels: enhancement

#255 - cggnn ROI creation is slow

Issue - State: closed - Opened by CarlinLiao 10 months ago
Labels: enhancement

#254 - Remove unused cg-gnn requirement from pyproject

Pull Request - State: closed - Opened by CarlinLiao 10 months ago - 2 comments

#254 - Remove unused cg-gnn requirement from pyproject

Pull Request - State: closed - Opened by CarlinLiao 10 months ago - 2 comments

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

Issue - State: closed - Opened by CarlinLiao 10 months ago
Labels: bug

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

Issue - State: closed - Opened by CarlinLiao 10 months ago
Labels: bug

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

Pull Request - State: closed - Opened by CarlinLiao 10 months ago
Labels: bug

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

Pull Request - State: closed - Opened by CarlinLiao 10 months ago
Labels: bug

#251 - `OnDemandRequester.get_counts_by_specimen` doesn't error if none of the cells selected are in a specimen it looks at

Issue - State: closed - Opened by CarlinLiao 10 months ago
Labels: bug

#251 - `OnDemandRequester.get_counts_by_specimen` doesn't error if none of the cells selected are in a specimen it looks at

Issue - State: closed - Opened by CarlinLiao 10 months ago
Labels: bug

#250 - Increase detail of analysis reproduction scripts

Issue - State: closed - Opened by jimmymathews 10 months ago
Labels: documentation, refactor

#250 - Increase detail of analysis reproduction scripts

Issue - State: closed - Opened by jimmymathews 10 months ago
Labels: documentation, refactor

#249 - Squidpy null bug

Pull Request - State: closed - Opened by jimmymathews 10 months ago - 1 comment

#249 - Squidpy null bug

Pull Request - State: closed - Opened by jimmymathews 10 months ago - 1 comment

#248 - Parallelize `cggnn` workflow

Pull Request - State: closed - Opened by CarlinLiao 10 months ago - 7 comments
Labels: refactor

#248 - Parallelize `cggnn` workflow

Pull Request - State: closed - Opened by CarlinLiao 10 months ago - 7 comments
Labels: refactor

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

Issue - State: closed - Opened by CarlinLiao 10 months ago - 2 comments
Labels: refactor

#246 - Slim down big table indexing

Pull Request - State: closed - Opened by jimmymathews 10 months ago - 1 comment

#246 - Slim down big table indexing

Pull Request - State: closed - Opened by jimmymathews 10 months ago - 1 comment

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

Pull Request - State: closed - Opened by jimmymathews 11 months ago

#244 - Add cg-gnn graph generation and plotting

Pull Request - State: closed - Opened by CarlinLiao 11 months ago - 7 comments
Labels: feature

#244 - Add cg-gnn graph generation and plotting

Pull Request - State: closed - Opened by CarlinLiao 11 months ago - 7 comments
Labels: feature

#243 - FeatureMatrixExtractor channel mismatch in live

Issue - State: closed - Opened by CarlinLiao 11 months ago - 19 comments
Labels: bug

#243 - FeatureMatrixExtractor channel mismatch in live

Issue - State: closed - Opened by CarlinLiao 11 months ago - 19 comments
Labels: bug

#242 - Deal with NF string processing for cggnn

Pull Request - State: closed - Opened by jimmymathews 11 months ago

#242 - Deal with NF string processing for cggnn

Pull Request - State: closed - Opened by jimmymathews 11 months ago

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

Issue - State: closed - Opened by CarlinLiao 11 months ago - 15 comments
Labels: bug

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

Issue - State: closed - Opened by CarlinLiao 11 months 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 11 months 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 11 months ago - 1 comment
Labels: enhancement

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

Issue - State: closed - Opened by CarlinLiao 11 months ago - 9 comments
Labels: enhancement

#238 - handle json-incompliant floats from OnDemandProvider

Pull Request - State: closed - Opened by CarlinLiao 11 months ago - 1 comment
Labels: enhancement

#238 - handle json-incompliant floats from OnDemandProvider

Pull Request - State: closed - Opened by CarlinLiao 11 months ago - 1 comment
Labels: enhancement

#237 - Implement timeout for ondemand computations

Pull Request - State: closed - Opened by jimmymathews 11 months ago

#236 - Reduce startup time for CLI scripts

Pull Request - State: closed - Opened by jimmymathews 11 months ago

#236 - Reduce startup time for CLI scripts

Pull Request - State: closed - Opened by jimmymathews 11 months ago

#235 - Bug fix to some db management

Pull Request - State: closed - Opened by jimmymathews 11 months ago

#235 - Bug fix to some db management

Pull Request - State: closed - Opened by jimmymathews 11 months ago

#234 - Database name

Issue - State: closed - Opened by jimmymathews 11 months ago - 1 comment
Labels: bug

#234 - Database name

Issue - State: closed - Opened by jimmymathews 11 months ago - 1 comment
Labels: bug

#233 - Update to support cg-gnn 0.2.1

Pull Request - State: closed - Opened by CarlinLiao 11 months ago - 13 comments
Labels: enhancement

#233 - Update to support cg-gnn 0.2.1

Pull Request - State: closed - Opened by CarlinLiao 11 months ago - 13 comments
Labels: enhancement

#232 - Supporting `cg-gnn` version 0.2

Issue - State: closed - Opened by CarlinLiao 11 months ago - 4 comments
Labels: enhancement

#232 - Supporting `cg-gnn` version 0.2

Issue - State: closed - Opened by CarlinLiao 11 months ago - 4 comments
Labels: enhancement

#231 - Test harness simplification

Issue - State: open - Opened by jimmymathews 11 months ago
Labels: development

#231 - Test harness simplification

Issue - State: closed - Opened by jimmymathews 11 months ago - 1 comment
Labels: development

#230 - Separate datasets for performance and modularity

Pull Request - State: closed - Opened by jimmymathews 11 months ago

#230 - Separate datasets for performance and modularity

Pull Request - State: closed - Opened by jimmymathews 11 months ago

#229 - Reduce CLI command setup time

Issue - State: closed - Opened by jimmymathews 11 months ago - 1 comment
Labels: bug

#229 - Reduce CLI command setup time

Issue - State: closed - Opened by jimmymathews 11 months ago - 1 comment
Labels: bug

#228 - Implement timeout for ondemand computations

Issue - State: closed - Opened by jimmymathews 11 months ago - 1 comment
Labels: bug, enhancement

#228 - Implement timeout for ondemand computations

Issue - State: closed - Opened by jimmymathews 11 months ago - 1 comment
Labels: bug, enhancement

#227 - cggnn workflow nextflow configuration

Pull Request - State: closed - Opened by CarlinLiao 11 months ago - 19 comments
Labels: feature

#227 - cggnn workflow nextflow configuration

Pull Request - State: closed - Opened by CarlinLiao 11 months ago - 19 comments
Labels: feature

#226 - Slim down expression quantification index

Issue - State: closed - Opened by jimmymathews 11 months ago - 1 comment
Labels: enhancement

#226 - Slim down expression quantification index

Issue - State: closed - Opened by jimmymathews 11 months ago - 1 comment
Labels: enhancement

#225 - Separate datasets as databases

Issue - State: closed - Opened by jimmymathews 11 months ago
Labels: enhancement

#225 - Separate datasets as databases

Issue - State: closed - Opened by jimmymathews 11 months ago
Labels: enhancement

#224 - Make substudy consistent for ondemand computed features.

Pull Request - State: closed - Opened by jimmymathews 11 months ago

#224 - Make substudy consistent for ondemand computed features.

Pull Request - State: closed - Opened by jimmymathews 11 months ago

#223 - Restore pending functionality for on-demand metrics

Issue - State: closed - Opened by jimmymathews 11 months ago - 1 comment
Labels: bug

#223 - Restore pending functionality for on-demand metrics

Issue - State: closed - Opened by jimmymathews 11 months ago - 1 comment
Labels: bug

#222 - Deprecate resource-intensive views

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

#222 - Deprecate resource-intensive views

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

#221 - Replace filesystem intermediate cache files

Issue - State: open - Opened by jimmymathews 12 months ago - 1 comment
Labels: feature, refactor

#221 - Replace filesystem intermediate cache files

Issue - State: closed - Opened by jimmymathews 12 months ago - 1 comment
Labels: feature, refactor

#220 - Work around memory limit problem

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

#220 - Work around memory limit problem

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

#219 - Memory limits during application initialization

Issue - State: closed - Opened by jimmymathews 12 months ago - 5 comments
Labels: bug, enhancement

#219 - Memory limits during application initialization

Issue - State: closed - Opened by jimmymathews 12 months ago - 5 comments
Labels: bug, enhancement

#218 - Null data values conversion to JSON

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

#218 - Null data values conversion to JSON

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

#217 - Visualization WIP

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

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

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

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

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

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

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

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

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

#214 - One delegate for initialization phase for ondemand services

Issue - State: closed - Opened by jimmymathews 12 months ago
Labels: bug

#214 - One delegate for initialization phase for ondemand services

Issue - State: closed - Opened by jimmymathews 12 months ago
Labels: bug

#213 - Possibly removing the "C" and "P" naming convention in feature columns

Issue - State: closed - Opened by jimmymathews 12 months ago - 2 comments
Labels: refactor, wontimplement

#213 - Possibly removing the "C" and "P" naming convention in feature columns

Issue - State: closed - Opened by jimmymathews 12 months ago - 2 comments
Labels: refactor, wontimplement

#212 - Vectorize FME pullers

Pull Request - State: closed - Opened by CarlinLiao 12 months ago - 31 comments
Labels: enhancement, refactor

#212 - Vectorize FME pullers

Pull Request - State: closed - Opened by CarlinLiao 12 months ago - 31 comments
Labels: enhancement, refactor

#211 - Get fraction of important cells expressing phenotype

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 35 comments
Labels: feature

#211 - Get fraction of important cells expressing phenotype

Pull Request - State: closed - Opened by CarlinLiao about 1 year ago - 35 comments
Labels: feature

#210 - small patches

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

#210 - small patches

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

#209 - final step to make cggnn importance scores available in sample-level features

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

#209 - final step to make cggnn importance scores available in sample-level features

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

#208 - hotfix cggnn scripts, streamline calls

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

#208 - hotfix cggnn scripts, streamline calls

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

#207 - `make test` distinguish between module and unit tests

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

#207 - `make test` distinguish between module and unit tests

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

#206 - `FeatureMatrixExtractor` should return DataFrames with `bool` values for channels and phenotypes instead of `int`

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

#205 - `PhenotypeCriteria` should not use `list` data structures

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

GitHub / nadeemlab/spt issues and pull requests