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
#357 - Adjust import workflow configuration to support S3
Pull Request -
State: closed - Opened by jimmymathews 1 day ago
#356 - Migration from spt-data
Pull Request -
State: closed - Opened by jimmymathews 1 day ago
#355 - Top results on study landing page, solicited from users
Issue -
State: open - Opened by jimmymathews 1 day ago
#354 - Compressed blobs caching
Issue -
State: open - Opened by jimmymathews 1 day ago
#353 - Some docs
Pull Request -
State: closed - Opened by jimmymathews 3 days ago
#352 - Make large datasets subsettable for UMAP
Issue -
State: open - Opened by jimmymathews 17 days ago
#351 - Issue154
Pull Request -
State: closed - Opened by jimmymathews 18 days ago
#350 - Supply UMAP position information as virtual slide
Pull Request -
State: closed - Opened by jimmymathews 26 days ago
- 2 comments
#349 - Add findings to study-summary endpoint
Pull Request -
State: closed - Opened by franciscouzo 29 days ago
- 1 comment
#348 - Too many null values in computed metrics
Issue -
State: open - Opened by jimmymathews about 1 month ago
Labels: bug
#347 - Fold findings endpoint into study summary
Issue -
State: closed - Opened by jimmymathews about 1 month ago
Labels: refactor
#346 - Fix MIME type header for importance-fraction-plot endpoint
Pull Request -
State: closed - Opened by franciscouzo about 1 month ago
- 1 comment
#345 - Add nonblocking counts endpoint
Pull Request -
State: closed - Opened by jimmymathews about 2 months ago
- 1 comment
#344 - Counts endpoint meant for polling
Issue -
State: closed - Opened by jimmymathews about 2 months ago
#343 - Refine Ripley metric extraction
Pull Request -
State: closed - Opened by jimmymathews about 2 months ago
#342 - Fix Ripley metric
Issue -
State: closed - Opened by jimmymathews about 2 months ago
#341 - Intermittent bug fixes
Pull Request -
State: closed - Opened by jimmymathews about 2 months ago
- 2 comments
#340 - Speed up with C extensions
Issue -
State: open - Opened by jimmymathews about 2 months ago
#339 - Infinite loop checking for completed metric
Issue -
State: closed - Opened by jimmymathews 2 months ago
- 2 comments
Labels: bug
#338 - Vectorize operations on CellDataArrays
Pull Request -
State: closed - Opened by CarlinLiao 2 months ago
- 11 comments
Labels: refactor
#337 - Operations over cell data arrays can be vectorized
Issue -
State: closed - Opened by CarlinLiao 2 months ago
- 3 comments
Labels: refactor
#336 - Partial caching
Issue -
State: open - Opened by jimmymathews 2 months ago
Labels: feature
#335 - Fix feature duplication bug
Pull Request -
State: closed - Opened by jimmymathews 2 months ago
- 1 comment
#334 - Cache GNN plots
Pull Request -
State: closed - Opened by jimmymathews 3 months ago
#333 - Cache GNN plot
Issue -
State: closed - Opened by jimmymathews 3 months ago
Labels: bug
#332 - Findings URLs
Issue -
State: closed - Opened by jimmymathews 3 months ago
- 1 comment
Labels: feature
#331 - Single-sample computation timeout
Issue -
State: closed - Opened by jimmymathews 3 months ago
Labels: bug
#330 - Feature identifier collision
Issue -
State: closed - Opened by jimmymathews 3 months ago
Labels: bug
#329 - Bug fix key conflict
Pull Request -
State: closed - Opened by jimmymathews 3 months ago
#328 - Remove unnecessary identifiers, causing concurrency conflicts
Issue -
State: closed - Opened by jimmymathews 3 months ago
Labels: bug
#327 - Parallelization refactor
Pull Request -
State: closed - Opened by jimmymathews 3 months ago
#326 - Make ondemand services parallelizable
Issue -
State: closed - Opened by jimmymathews 3 months ago
- 2 comments
Labels: refactor
#325 - Move plugin repos into this main repo
Pull Request -
State: closed - Opened by CarlinLiao 4 months ago
- 3 comments
Labels: refactor
#324 - Issue314
Pull Request -
State: closed - Opened by jimmymathews 4 months ago
#323 - Consolidating by bringing in spt plugin repository contents
Issue -
State: closed - Opened by jimmymathews 4 months ago
Labels: refactor
#322 - Library dependency updates
Pull Request -
State: closed - Opened by jimmymathews 4 months ago
- 3 comments
#321 - Reduce memory footprint with an optimization in cache checking
Pull Request -
State: closed - Opened by jimmymathews 4 months ago
#320 - Make GNN plots available as an SPT CLI command and API endpoint
Pull Request -
State: closed - Opened by CarlinLiao 5 months ago
- 9 comments
Labels: feature
#319 - Make GNN plots available as an SPT CLI command and API endpoint
Issue -
State: closed - Opened by CarlinLiao 5 months ago
- 7 comments
Labels: feature
#318 - Implement a refresh signal for the ondemand containers
Issue -
State: closed - Opened by jimmymathews 5 months ago
- 2 comments
Labels: wontfix, feature
#317 - Support normalized case for study names
Issue -
State: open - Opened by jimmymathews 5 months ago
- 1 comment
Labels: feature
#316 - Study sets
Pull Request -
State: closed - Opened by jimmymathews 5 months ago
#315 - Implement cell limit for cells data query
Pull Request -
State: closed - Opened by jimmymathews 5 months ago
#314 - Stalled backend for large cell data payloads
Issue -
State: closed - Opened by jimmymathews 5 months ago
- 2 comments
Labels: bug
#313 - scverse ecosystem-package and ADI/SpatialData conversion
Issue -
State: open - Opened by sanadeem 5 months ago
Labels: feature
#312 - Study sets
Issue -
State: closed - Opened by jimmymathews 5 months ago
Labels: feature
#311 - Update reanalysis scripts
Pull Request -
State: closed - Opened by jimmymathews 6 months ago
#310 - More study detail from API service
Pull Request -
State: closed - Opened by jimmymathews 6 months ago
#309 - Additional study details
Issue -
State: closed - Opened by jimmymathews 6 months ago
- 1 comment
Labels: feature
#308 - Failing metric fails to cancel
Issue -
State: closed - Opened by jimmymathews 6 months ago
- 2 comments
Labels: bug, wontfix
#307 - add graph plugin plot code
Pull Request -
State: closed - Opened by CarlinLiao 7 months ago
- 14 comments
Labels: enhancement
#306 - Add graph plugin heatmaps
Issue -
State: closed - Opened by CarlinLiao 7 months ago
Labels: enhancement
#305 - Pin workflow image tag default to current SPT version
Pull Request -
State: closed - Opened by CarlinLiao 7 months ago
- 3 comments
Labels: refactor
#304 - Upload importance should be generated procedurally in Nextflow workflows
Issue -
State: open - Opened by CarlinLiao 7 months ago
Labels: enhancement
#303 - SPT image version isn't pinned
Issue -
State: closed - Opened by CarlinLiao 7 months ago
- 1 comment
Labels: bug
#302 - Implements sorting by default on most endpoints
Pull Request -
State: closed - Opened by jimmymathews 7 months ago
#301 - Include utility for feature deletion
Pull Request -
State: closed - Opened by jimmymathews 7 months ago
#300 - Utility to delete one feature
Issue -
State: closed - Opened by jimmymathews 7 months ago
- 1 comment
Labels: enhancement
#299 - Implement cell-level api endpoint
Pull Request -
State: closed - Opened by jimmymathews 7 months ago
#298 - Cell level data
Issue -
State: closed - Opened by jimmymathews 7 months ago
- 5 comments
Labels: feature
#297 - add new specifiers to DataAccessor importance
Pull Request -
State: closed - Opened by CarlinLiao 7 months ago
Labels: enhancement
#296 - Analysis replication DataAccessor is missing new importance score specifiers
Issue -
State: closed - Opened by CarlinLiao 7 months ago
Labels: enhancement
#295 - Counts files to db migration
Pull Request -
State: closed - Opened by wooferclaw 8 months ago
- 4 comments
#294 - Quick patch to counts_by_signature to handle if one of positive or negative is empty
Pull Request -
State: closed - Opened by CarlinLiao 8 months ago
- 1 comment
Labels: bug
#293 - `DataAccessor.counts_by_signature` fails if either no positive or no negative markers are provided
Issue -
State: closed - Opened by CarlinLiao 8 months ago
Labels: bug
#292 - Add support for graph-transformer plugin
Pull Request -
State: closed - Opened by CarlinLiao 8 months ago
- 7 comments
Labels: enhancement
#291 - Modularize workflow Nextflow files
Pull Request -
State: closed - Opened by CarlinLiao 8 months ago
Labels: enhancement, refactor
#290 - Balance graph datasets
Issue -
State: open - Opened by CarlinLiao 8 months ago
Labels: enhancement
#289 - Modularize graphs workflow
Issue -
State: closed - Opened by CarlinLiao 8 months ago
Labels: refactor
#288 - prevent package caching in Docker images
Pull Request -
State: closed - Opened by CarlinLiao 8 months ago
- 1 comment
Labels: enhancement
#287 - Make `spt workflow configure` support both Docker and Singularity
Pull Request -
State: closed - Opened by CarlinLiao 8 months ago
- 20 comments
Labels: enhancement
#286 - Expand workflow configure support for singularity
Issue -
State: closed - Opened by CarlinLiao 8 months ago
- 1 comment
Labels: enhancement
#285 - No option to show Nextflow logs when running the test suite
Issue -
State: closed - Opened by CarlinLiao 9 months ago
- 4 comments
Labels: development
#284 - Allow saved graphs to be readable without importing spatialprofilingtoolbox
Issue -
State: closed - Opened by CarlinLiao 9 months ago
- 1 comment
Labels: refactor
#283 - Convert cggnn/graphs and workflow configure to use config files (redo)
Pull Request -
State: closed - Opened by CarlinLiao 9 months ago
- 17 comments
Labels: refactor
#282 - Dockerize `spt cggnn train` (redo)
Pull Request -
State: closed - Opened by CarlinLiao 9 months ago
- 1 comment
Labels: enhancement
#281 - Convert cggnn/graphs and workflow configure to use config files
Pull Request -
State: closed - Opened by CarlinLiao 9 months ago
- 8 comments
Labels: refactor
#280 - Save adjacency matrices separately
Pull Request -
State: closed - Opened by CarlinLiao 9 months ago
- 1 comment
Labels: bug
#279 - scipy sparse matrix compatibility issues
Issue -
State: closed - Opened by CarlinLiao 9 months ago
Labels: bug
#278 - Refactor `spt workflow configure` to accept a generic configuration file instead of CLI arguments
Issue -
State: closed - Opened by CarlinLiao 9 months ago
- 1 comment
Labels: refactor
#277 - Rename `cg-gnn` submodule to `graphs`
Issue -
State: closed - Opened by CarlinLiao 9 months ago
- 4 comments
Labels: duplicate, refactor
#276 - Dockerize `spt cggnn train`
Pull Request -
State: closed - Opened by CarlinLiao 9 months ago
- 12 comments
#275 - Dockerization of the `cg-gnn` model
Issue -
State: closed - Opened by CarlinLiao 9 months ago
- 4 comments
Labels: duplicate, refactor
#274 - Would adding ` --no-cache-dir` to pip install commands slim down Docker image sizes?
Issue -
State: closed - Opened by CarlinLiao 9 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 10 months ago
- 4 comments
Labels: refactor
#272 - Abstract out graph deep learning functionality to an external plugin system
Issue -
State: closed - Opened by CarlinLiao 10 months ago
- 9 comments
Labels: refactor
#271 - Compartmentalize dependency on DGL and torch to cg-gnn model
Issue -
State: closed - Opened by CarlinLiao 10 months ago
- 2 comments
Labels: refactor
#270 - replace histocartography with cg-gnn submodule
Pull Request -
State: closed - Opened by CarlinLiao 10 months ago
#269 - Convert `cg-gnn`/`histocartography` to a git submodule
Issue -
State: closed - Opened by CarlinLiao 10 months ago
- 6 comments
Labels: enhancement
#268 - Add tmi2022 GNN model
Issue -
State: closed - Opened by CarlinLiao 10 months ago
- 6 comments
Labels: enhancement
#267 - adjust specimen allocation
Pull Request -
State: closed - Opened by CarlinLiao 10 months ago
- 9 comments
Labels: enhancement
#266 - Stabilize GNN training/validation/test set creation when given bimodal specimen sizes
Issue -
State: closed - Opened by CarlinLiao 10 months ago
Labels: enhancement
#265 - Add urothelial dataset run results
Issue -
State: closed - Opened by jimmymathews 10 months ago
- 1 comment
#264 - il2 importance analysis
Pull Request -
State: closed - Opened by CarlinLiao 10 months ago
- 5 comments
Labels: enhancement
#263 - Add importance score evaluations to analysis_replication
Issue -
State: closed - Opened by CarlinLiao 10 months ago
Labels: enhancement
#262 - Add rigorous checks for analysis reproduction
Pull Request -
State: closed - Opened by jimmymathews 10 months ago
#261 - fix cggnn nextflow on small specimens
Pull Request -
State: closed - Opened by CarlinLiao 10 months ago
Labels: bug
#261 - fix cggnn nextflow on small specimens
Pull Request -
State: closed - Opened by CarlinLiao 10 months ago
Labels: bug
#260 - cggnn workflow errors if no graphs are created from a specimen
Issue -
State: closed - Opened by CarlinLiao 10 months ago
- 5 comments
Labels: bug
#260 - cggnn workflow errors if no graphs are created from a specimen
Issue -
State: closed - Opened by CarlinLiao 10 months ago
- 5 comments
Labels: bug