theislab/CellFlow

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Modeling complex perturbations with CellFlow

Stars: 159
Forks: 27
Open beginner issues: 0
Indexed issues: 50

Dominant language: Python
License: MIT
Last GitHub push: Jul 12, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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50 open issues indexed

PolyForm license in pyproject.toml Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 68/100

theislab/CellFlow#311 · Opened Jul 27, 2026
How to improve prediction speed? Open

bug

Difficulty 5/5 Over a week Newbie friendliness 35/100

theislab/CellFlow#289 · 1 comment · Opened Mar 5, 2026
Why high dropout on the conditional embedding Open

question

Difficulty 3/5 1-2 days Newbie friendliness 25/100

theislab/CellFlow#277 · 3 comments · Opened Sep 1, 2025
Fix test `test_cellflow_with_validation` for GENOT Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 25/100

theislab/CellFlow#273 · Opened Aug 6, 2025
Accessibility of trained models Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

theislab/CellFlow#269 · 1 comment · Opened Aug 4, 2025
Fix `predict_batch` Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 20/100

theislab/CellFlow#265 · Opened Jul 25, 2025
Update iNeuron tutorial Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

theislab/CellFlow#263 · Opened Jul 23, 2025
batched predict also for `PredictionSampler` Open

enhancement

theislab/CellFlow#251 · 1 assignee · Opened Jun 13, 2025
Torch backend implementation Open

enhancement

theislab/CellFlow#248 · 2 comments · 4 assignees · Opened May 28, 2025
add different time sampling Open

enhancement

theislab/CellFlow#232 · 1 assignee · Opened May 8, 2025
alternative time encoder module Open

enhancement

theislab/CellFlow#231 · 1 assignee · Opened May 8, 2025
Applicability for vanilla differential expression testing Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 15/100

theislab/CellFlow#221 · 1 comment · Opened Apr 24, 2025
New `PCADecodedMetrics2` callback Open

enhancement

theislab/CellFlow#220 · 1 comment · 1 assignee · Opened Apr 23, 2025
More interpretable error in `get_esm_embedding` Open

enhancement

theislab/CellFlow#211 · 3 comments · 1 assignee · Opened Apr 15, 2025
adapting `_validation_step` Open

enhancement

theislab/CellFlow#199 · 1 assignee · Opened Apr 4, 2025
Removal of `encode_conditions` Open

structural change

theislab/CellFlow#197 · 1 assignee · Opened Apr 4, 2025
Example notebook on how to write custom callbacks Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 42/100

theislab/CellFlow#195 · Opened Apr 2, 2025
Proper documentation for cellflow.metrics Open

enhancement

theislab/CellFlow#190 · 1 assignee · Opened Mar 31, 2025
re-enable linting of docs in workflows/lint.yml Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

theislab/CellFlow#169 · Opened Mar 11, 2025
enable dataset size check in cfp.datasets Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

theislab/CellFlow#167 · Opened Mar 7, 2025
building docs we cannot include cfp.pp because of cuml Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

theislab/CellFlow#161 · Opened Mar 5, 2025
suppress inherited attributes and methods from docs , e.g. flax and scVI, which we don't need. Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

theislab/CellFlow#149 · Opened Feb 24, 2025
`AttributeError: 'tuple' object has no attribute 'divergence'` Open

bug

theislab/CellFlow#133 · 1 assignee · Opened Nov 6, 2024
Output of `predict` Open

bug

theislab/CellFlow#129 · 2 comments · 1 assignee · Opened Nov 1, 2024
`condition_id_key` also in DataManager Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

theislab/CellFlow#120 · Opened Oct 2, 2024
Improve docs in scvi external + more tests. As of now, only focused on making VAE work with normal likelihood Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

theislab/CellFlow#119 · Opened Oct 1, 2024
correct type in docs + say what happens when `None` Open

Difficulty 1/5 1-3 hours Newbie friendliness 58/100

theislab/CellFlow#111 · Opened Sep 11, 2024
centered_pca result cannot be saved in h5ad Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

theislab/CellFlow#108 · 2 comments · Opened Sep 9, 2024
improve docs in `centered_pca` Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

theislab/CellFlow#107 · Opened Sep 9, 2024
fixing dependencies Open

bug

theislab/CellFlow#104 · 1 assignee · Opened Aug 29, 2024
joyplot Open

enhancement

theislab/CellFlow#102 · 1 assignee · Opened Aug 29, 2024
adaptation to callbacks Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

theislab/CellFlow#101 · Opened Aug 29, 2024
save predictions to adata, and add multiple push-forwards for GENOT, provide downstream functionality for uncertainties Open

enhancement

theislab/CellFlow#92 · 1 assignee · Opened Aug 27, 2024
remove `to_boolean` in `prepare` Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 30/100

theislab/CellFlow#89 · Opened Aug 27, 2024
do not reset logs when continuing training. Open

enhancement

theislab/CellFlow#88 · 2 comments · 2 assignees · Opened Aug 23, 2024
Implementation of `cfp.pp.get_gene_embedding_from_esm` Open

enhancement

theislab/CellFlow#87 · 1 comment · 1 reaction · 1 assignee · Opened Aug 23, 2024
Only compute val predictions whenever we have a callback. Open

enhancement

theislab/CellFlow#85 · 1 assignee · Opened Aug 23, 2024
make samplers compatible with unconditional data Open

enhancement

theislab/CellFlow#74 · 1 assignee · Opened Aug 19, 2024
check whether we can remove `self._covar_to_idx` in `DataManager` Open

enhancement

theislab/CellFlow#63 · 1 assignee · Opened Aug 12, 2024
add regression tests Open

test

Difficulty 4/5 3-5 days Newbie friendliness 20/100

theislab/CellFlow#47 · Opened Aug 8, 2024
adapt plotting function to new `predict` Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 25/100

theislab/CellFlow#45 · Opened Aug 8, 2024
warning/option for integer perturbation covariate keys Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

theislab/CellFlow#44 · Opened Aug 8, 2024
enable passing callables to aggregation function and metrics Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

theislab/CellFlow#37 · Opened Aug 1, 2024
Make validation step more efficient Open

enhancement

theislab/CellFlow#35 · 1 assignee · Opened Aug 1, 2024
unify warnings/loggings. Open

enhancement

theislab/CellFlow#34 · 1 comment · 1 assignee · Opened Jul 31, 2024
test `plot_embedding` Open

test

theislab/CellFlow#15 · 1 assignee · Opened Jul 17, 2024
more tests for data loading Open

enhancement test

theislab/CellFlow#10 · 1 assignee · Opened Jul 15, 2024
Resolve pre-commit errors Open

enhancement

theislab/CellFlow#9 · 3 assignees · Opened Jul 15, 2024
setup docs Open

enhancement

theislab/CellFlow#8 · 1 assignee · Opened Jul 15, 2024
How to do masking Open

enhancement

theislab/CellFlow#2 · 7 comments · 1 assignee · Opened Jul 12, 2024

theislab/CellFlow

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