Ecosyste.ms: Issues

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

GitHub / theislab/pertpy issues and pull requests

#489 - Add DE set comparisons

Pull Request - State: closed - Opened by Zethson about 1 year ago - 1 comment
Labels: enhancement, chore

#488 - More informative images in tutorial gallery

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

#487 - Add perturbation space tutorial

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

#486 - DE set comparisons

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

#485 - Replace Tutorial Icons

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

#484 - Improving logging

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

#483 - Expand metadata support for enrichment

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

#482 - Add enrichment

Pull Request - State: closed - Opened by Zethson about 1 year ago - 1 comment
Labels: enhancement, chore

#481 - Save perturbation and clustering labels as categorical

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

#480 - Add Drug metadata from chembl

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

#479 - Improve annotate docstring in cell line

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

#478 - Metadata classes should load data more lazily

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

#477 - Add DE filtering

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

#476 - Consistent links to tutorials in the docs

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

#475 - Fix/discriminator classifier nn dimensions

Pull Request - State: closed - Opened by Lilly-May about 1 year ago - 2 comments
Labels: bug

#474 - Improve tool explanations in docs

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

#473 - Optimize from_scanpy

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

#472 - Fix subsetting of milo.plot_da_beeswarm

Pull Request - State: closed - Opened by Lilly-May about 1 year ago - 1 comment
Labels: bug

#471 - PertSpace docs improvements

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

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

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

#469 - Adapt cell line API + notebook

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

#468 - Discriminator classifier throws errors due to mismatched neural network dimensions

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

#467 - Add simple gene set enrichment for various metadata types

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

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

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

#465 - Docs improvements for perturbation space

Pull Request - State: closed - Opened by Lilly-May about 1 year ago
Labels: enhancement

#464 - Make dialogue's load protected

Pull Request - State: closed - Opened by Lilly-May about 1 year ago
Labels: enhancement

#463 - Consistent API: Dialogue's load method

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

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

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

#461 - Add combosciplex dataloader

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

#460 - fix: double plot issue related to barplot

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

#459 - Update all tutorials with new API

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

#458 - Harmonize plotting API

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

#457 - Error when subsetting nhoods in pertpy.plot.milo.da_beeswarm

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

#456 - New plotting API

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

#455 - CentroidSpace AnnData Annotations

Pull Request - State: closed - Opened by Lilly-May about 1 year ago - 3 comments
Labels: bug

#454 - sccoda.run_nuts fails with new jax release

Issue - State: closed - Opened by Lilly-May about 1 year ago - 4 comments
Labels: bug

#453 - DiscriminatorClassifier compatibility with sparse matrices

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

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

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

#451 - Update DIALOGUE dataset

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

#450 - Added smillie_2019 dataloader and renamed smillie dataset to tasccoda_example

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

#449 - Augur breaks with certain versions

Issue - State: closed - Opened by yugeji about 1 year ago - 2 comments
Labels: bug

#448 - Restructure the plotting API

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

#447 - Add plotting example output to every plotting function

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

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

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

#445 - optimising "from_scanpy" function

Pull Request - State: closed - Opened by kcArtemis about 1 year ago - 5 comments

#444 - Add moa and compound annotation

Pull Request - State: closed - Opened by wxicu about 1 year ago - 1 comment
Labels: enhancement, chore

#443 - Removed scGen batch removal tutorial from gallery

Pull Request - State: closed - Opened by Lilly-May about 1 year ago - 2 comments
Labels: chore

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

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

#441 - Replace plotnine implementation of barplot with seaborn/matplotlib

Pull Request - State: closed - Opened by kcArtemis over 1 year ago - 4 comments

#440 - Update _mixscape.py

Pull Request - State: closed - Opened by kcArtemis over 1 year ago - 1 comment

#439 - Upload smillie dataset to figshare

Issue - State: closed - Opened by Zethson over 1 year ago
Labels: enhancement

#438 - Speedup base coda load

Issue - State: closed - Opened by Zethson over 1 year ago - 2 comments
Labels: enhancement

#437 - Test_simple_perturbation_space

Pull Request - State: closed - Opened by Lilly-May over 1 year ago - 1 comment
Labels: bug

#436 - test_simple_perturbation_space.py fails

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

#435 - Hackathon metrics

Pull Request - State: open - Opened by Zethson over 1 year ago - 1 comment

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

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

#433 - Docs examples for CINEMA-OT

Pull Request - State: closed - Opened by Lilly-May over 1 year ago - 1 comment
Labels: enhancement

#432 - Fix code coverage

Pull Request - State: closed - Opened by flying-sheep over 1 year ago - 1 comment
Labels: bug

#431 - old codecov config

Pull Request - State: closed - Opened by Zethson over 1 year ago

#430 - Improve pytest speed

Issue - State: open - Opened by Zethson over 1 year ago - 1 comment
Labels: enhancement, performance

#429 - scgen test fails with matplotlib AttributeError

Issue - State: closed - Opened by Zethson over 1 year ago - 2 comments
Labels: bug

#428 - codecov not working anymore

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

#427 - Add classifiers

Pull Request - State: closed - Opened by Zethson over 1 year ago

#426 - Removing dependencies

Pull Request - State: closed - Opened by Zethson over 1 year ago - 1 comment
Labels: enhancement

#425 - Minimize dependencies

Issue - State: closed - Opened by Zethson over 1 year ago
Labels: enhancement

#424 - Cinemaot dataset loader

Pull Request - State: closed - Opened by Lilly-May over 1 year ago - 2 comments

#423 - Added example for pt.pl.milo.nhood_graph

Pull Request - State: closed - Opened by Lilly-May over 1 year ago
Labels: enhancement

#422 - scope imports of ete3 in tasccoda

Pull Request - State: closed - Opened by Zethson over 1 year ago - 1 comment
Labels: enhancement

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

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

#420 - pertpy cannot be imported on windows

Issue - State: open - Opened by pandaqiuqiu over 1 year ago - 5 comments
Labels: bug, windows

#419 - Add cinemaot nb

Pull Request - State: closed - Opened by Zethson over 1 year ago
Labels: enhancement, chore

#418 - actually use `neighbors_key` in `milo`

Pull Request - State: closed - Opened by maarten-devries over 1 year ago

#416 - Streamlining Distance API

Issue - State: open - Opened by Zethson over 1 year ago - 5 comments
Labels: enhancement

#415 - Improve GPU support for scgen

Issue - State: open - Opened by Zethson over 1 year ago
Labels: enhancement

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

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

#413 - Fixed some bugs (due to inconsistencies during migration) and typos in CINEMA-OT

Pull Request - State: closed - Opened by MingzeDong over 1 year ago - 1 comment

#412 - Synchronous dataloader write fails

Issue - State: open - Opened by yugeji over 1 year ago - 1 comment
Labels: bug

#411 - Fixed set_fdr for tascCODA models

Pull Request - State: closed - Opened by Lilly-May over 1 year ago - 1 comment
Labels: bug, chore

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

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

#409 - Small bug fixes and docs improvements

Pull Request - State: closed - Opened by Lilly-May over 1 year ago - 1 comment
Labels: bug

#408 - pt.pl.milo.nhood_graph throws StopIteration error

Issue - State: closed - Opened by Lilly-May over 1 year ago - 8 comments
Labels: bug

#407 - pt.tl.tascCODA.set_fdr() throws ValueError

Issue - State: closed - Opened by Lilly-May over 1 year ago
Labels: bug

#406 - Fixture for Augur tests

Pull Request - State: closed - Opened by Lilly-May over 1 year ago - 1 comment
Labels: enhancement

#405 - Consistent API experience

Issue - State: closed - Opened by Zethson over 1 year ago - 6 comments
Labels: enhancement

#404 - fix Implicit modification warnings in cellline tests

Pull Request - State: closed - Opened by wxicu over 1 year ago - 1 comment

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

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

#402 - cannot import sccoda with reticulate

Issue - State: closed - Opened by adityamahadevaniyer over 1 year ago - 11 comments
Labels: bug, coda

#401 - Remove remotezip

Pull Request - State: closed - Opened by wxicu over 1 year ago - 1 comment

#400 - Add docstring examples for CINEMA-OT

Issue - State: closed - Opened by Zethson over 1 year ago
Labels: enhancement

#399 - Add docstring example for pertpy.plot.coda.effects_umap

Issue - State: closed - Opened by Zethson over 1 year ago
Labels: enhancement

#398 - Speed up tests by subsampling

Pull Request - State: closed - Opened by Lilly-May over 1 year ago - 2 comments
Labels: enhancement, chore

#397 - bug fixes, implementation tweaks, and additional distances

Pull Request - State: closed - Opened by yugeji over 1 year ago - 3 comments
Labels: bug, chore

#396 - Move to new numpy.random.Generator

Pull Request - State: closed - Opened by Lilly-May over 1 year ago - 1 comment
Labels: bug, chore

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

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

#394 - pertpy v.0.5.0 not compatible with anndata v.0.10.0

Issue - State: closed - Opened by lucas-diedrich over 1 year ago - 3 comments
Labels: bug

#393 - Installation Apple Silicon

Pull Request - State: closed - Opened by Lilly-May over 1 year ago
Labels: chore

#392 - Fix cinema OT test

Pull Request - State: closed - Opened by Zethson over 1 year ago
Labels: bug

#391 - Documentation examples

Pull Request - State: closed - Opened by Lilly-May over 1 year ago
Labels: enhancement