Drift correction#58
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…29) * 🚧 start collecting dataframe schemas with enrichment analysis result * ✨ ensure valid numeric omics data functionality * 🚧 add schema validation to examples - can be added to function call using `pa.check_types` * 🐛 add missing dependency * 🐛 bool and boolean with NANs are not the same for pandera. * 🐛 fix tests (convert dtypes expect bool) * 🚧 Add and align differential analysis schema - ANOVA descriptive statistis seems to have errors - should missing values for p-values be allowed? * 🐛 leave strings as they are * 🚧 build schema on the fly for numeric data - could be used to give specific feedback on user provided columns * 🎨 add pandera to mapped types of other libraries * 🚧 add Schemas to functions - anova has two return types depending on number of groups... * 🚧 add two schemas to anova function Schemas should be unified eventually * 📝 all commands for local execution of docs ... as integration test * 🐛 remove testing shell script to find errors in action runs (for automation) * ✨ construct types for exploratory analysis - create a separate PR to refactor exploratory analysis module * 🎨 add Sebastians hint on BaseModel visualization * 🎨 clean-up types - formatting was not done properly in docs - not used as a composite type as of now
* ✨ custom PR template for new module * 🎨 highlight only folder name * 📝 propose to use built-in virtual environment * 📝 some more design hints * 📝 any docstring type for functions is fine * 🎨 remove intermediate heading * 📝 add hint on using example data for api examples * Update .github/workflows/PULL_REQUEST_TEMPLATE/module.md --------- Co-authored-by: feliciaschulz <112621625+feliciaschulz@users.noreply.github.com>
* 🔧 remove constraint on numpy as latest inmoose does nto require it anymore * 🔧 align github actions to python package template ... as for other librarier * 🎨 format toml with even better toml * 🔧 isort and ruff configuration - turn ruff configuration on in a separate PR * 🎨 format src folder * 🎨 apply ruff check autofixes * 🔥 remove tox artefacts * 🚚 rename actions yaml file * 🎨 isort tests
* 🚚 separate batch correction from normalization - fix Move batch correction outside Normalisation 💄 Fixes #22 * 🐛 sync normalization nb and update test imports * 🎨 format and remove unused import * 🐛 sync nb * 🐛 add batch correction to website index * 🎨 link module api
* 🎨 move from rst to md * 🚧 Close clean up conf.py Fixes #21 - remove duplication - sort code as in other packages - double check if additional entries wer needed
* 🎨 consistent scaling and naming - apply standardization before PCA (leads to minor change in axis) - talk about batch correction, not normalization * 🎨 shorten titles * 🎨 order more meaningfully
* 📝 add Contributing.md as reference to PR template * 🐛 make it an url
* 🚧 process metabolomics example data * 🎨 format * ✨ tested data with ANOVA, finish processing of data
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
…ving temp name column before returning df, raising ValueError with wrong QC threshold
- hide long source cells - few typos found by copilot - split long lines using rewrap tool
… Minor other changes in documentation of notebook.
- anyway not optional, so just set defaults
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This pull request introduces a new API usage example for metabolomics data filtering and makes minor updates to the documentation and existing notebooks. The main addition is a comprehensive Jupyter notebook (and paired Python script) demonstrating how to filter metabolomics data using the
acorepackage. There are also small metadata and index updates.New API Example: Metabolomics Data Filtering
filter_metabolomics.ipynband paired scriptfilter_metabolomics.pydemonstrating:Documentation and Index Updates
index.mdto include the new filtering example and another drift correction example in the API usage section.normalization_analysis.py(Jupytext version update).batch_correction.ipynbfor consistency; no content changes. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20]These updates expand the documentation with a practical filtering workflow for metabolomics data and ensure the API examples are easily discoverable.<!--
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