krishnanlab/PyGenePlexus issues and pull requests

#332 - updated tst to res and code comments

Pull Request - State: closed - Opened by ChristopherMancuso 8 days ago

#331 - multiple updates to CLI

Pull Request - State: closed - Opened by ChristopherMancuso 19 days ago

#330 - Fixes to setters and custom

Pull Request - State: closed - Opened by ChristopherMancuso about 2 months ago

#329 - fix custom options

Issue - State: closed - Opened by ChristopherMancuso about 2 months ago - 1 comment
Labels: bug

#328 - Zenodo and downloads

Pull Request - State: closed - Opened by ChristopherMancuso about 2 months ago

#327 - looking into network edge thresholds

Issue - State: open - Opened by ChristopherMancuso about 2 months ago
Labels: enhancement

#326 - convert task to more readable may break code

Issue - State: closed - Opened by ChristopherMancuso 2 months ago
Labels: bug

#325 - Api functionality updates

Pull Request - State: closed - Opened by ChristopherMancuso 2 months ago

#324 - get list of genes that is important for similairty tables

Issue - State: open - Opened by ChristopherMancuso 2 months ago
Labels: enhancement

#323 - simultaneously run two species

Issue - State: open - Opened by ChristopherMancuso 2 months ago
Labels: enhancement

#322 - Reproducibility and Documentation

Issue - State: open - Opened by ChristopherMancuso 2 months ago - 1 comment
Labels: documentation, Tests

#321 - allow users to specify negatives

Issue - State: closed - Opened by ChristopherMancuso 2 months ago - 2 comments

#320 - property and setter decorators broken

Issue - State: closed - Opened by ChristopherMancuso 2 months ago
Labels: bug

#319 - CLI does save isolated genes

Issue - State: closed - Opened by ChristopherMancuso 2 months ago
Labels: bug

#318 - number of file limit in Zenodo

Issue - State: closed - Opened by ChristopherMancuso 2 months ago - 1 comment
Labels: bug

#317 - add one-to-one orthologs for cross species transfer predictions

Issue - State: closed - Opened by ChristopherMancuso 2 months ago - 1 comment

#316 - a gene name to input gene conversion table

Issue - State: closed - Opened by ChristopherMancuso 2 months ago - 3 comments

#315 - a gsc description for similarities results

Issue - State: closed - Opened by ChristopherMancuso 2 months ago - 1 comment

#314 - change cv results for small genesets

Issue - State: closed - Opened by ChristopherMancuso 2 months ago - 5 comments

#313 - Mondo and prop

Pull Request - State: closed - Opened by ChristopherMancuso 6 months ago

#312 - Bump pystow from 0.5.0 to 0.5.4

Pull Request - State: open - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#311 - added check if Entrez might not be correct species

Pull Request - State: closed - Opened by ChristopherMancuso 8 months ago

#310 - Bump pytest-mock from 3.11.1 to 3.14.0

Pull Request - State: open - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#309 - basic api runs with all parameters

Pull Request - State: closed - Opened by ChristopherMancuso 8 months ago

#308 - Bump pystow from 0.5.0 to 0.5.3

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#307 - change making sim dfs only from GSC

Pull Request - State: closed - Opened by ChristopherMancuso 9 months ago

#306 - Bump scikit-learn from 1.3.0 to 1.4.1.post1

Pull Request - State: open - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#305 - Bump tqdm from 4.65.0 to 4.66.2

Pull Request - State: open - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#304 - Bump numpy from 1.23.5 to 1.26.4

Pull Request - State: open - Opened by dependabot[bot] 10 months ago
Labels: dependencies

#303 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] 10 months ago

#302 - Bump scikit-learn from 1.3.0 to 1.4.0

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#301 - Add sp_trn and sp_tst options

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

#300 - Bump scikit-learn from 1.3.0 to 1.3.2

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#299 - Bump pystow from 0.5.0 to 0.5.2

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#298 - Bump pytest-mock from 3.11.1 to 3.12.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#297 - Bump numpy from 1.23.5 to 1.26.3

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#296 - update rtd config

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

#295 - Bump tox from 4.6.4 to 4.11.4

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#294 - Bump numpy from 1.23.5 to 1.26.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#293 - Bump tox from 4.6.4 to 4.11.3

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 2 comments
Labels: dependencies

#292 - Bump tox from 4.6.4 to 4.11.2

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#291 - Bump pytest from 7.2.0 to 7.4.2

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#290 - Bump tox from 4.6.4 to 4.11.1

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#289 - Bump pytest from 7.2.0 to 7.4.1

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#288 - changed to using sphinx.ext.napoleon not sphinxcontrib.napoleon

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

#287 - Bump tox from 4.6.4 to 4.11.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#286 - Bump tox from 4.6.4 to 4.10.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#285 - Bump tox from 4.6.4 to 4.9.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#284 - Bump tox from 4.6.4 to 4.8.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#283 - Bump tqdm from 4.65.0 to 4.66.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#282 - Bump tqdm from 4.65.0 to 4.66.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#281 - Bump tqdm from 4.65.0 to 4.65.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#280 - Bump tox from 4.6.4 to 4.7.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#279 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#278 - Bump numpy from 1.23.5 to 1.25.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#277 - Fix way DisGeNet annotations are being added

Issue - State: closed - Opened by ChristopherMancuso over 1 year ago - 1 comment
Labels: bug

#276 - Bump pyyaml from 6.0 to 6.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#275 - Bump pytest from 7.2.0 to 7.4.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#274 - Bump tqdm from 4.64.1 to 4.65.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#273 - Bump pystow from 0.4.7 to 0.5.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#272 - Bump pytest-order from 1.0.1 to 1.1.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#271 - Bump requests-mock from 1.10.0 to 1.11.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#270 - Bump pytest-mock from 3.10.0 to 3.11.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#269 - Bump pytest-cov from 4.0.0 to 4.1.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#268 - Bump parameterized from 0.8.1 to 0.9.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#267 - Bump tox from 3.27.1 to 4.6.4

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#266 - Bump numpy from 1.23.5 to 1.25.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#265 - Bump sphinx from 5.3.0 to 7.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#264 - Bump sphinx-autodoc-typehints from 1.19.5 to 1.23.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#263 - Bump scikit-learn from 1.1.3 to 1.3.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#262 - Bump requests from 2.28.1 to 2.31.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#261 - Bump tox from 3.27.1 to 4.4.6

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies