v0.0.1

What's Changed

Initial release

Breaking Changes

• Unify anndata handling 6 | alphatools.pp.scanpy_pycombat by @lucas-diedrich in #90
• Unify anndata handling 5 | alphatools.pp.impute_gaussian by @lucas-diedrich in #89
• Unify anndata handling 4 | alphatools.pp.normalize by @lucas-diedrich in #88
• Unify anndata handling 3 | alphatools.pp.nanlog by @lucas-diedrich in #86
• Unify anndata handling 2 | at.pp.scale_and_center by @lucas-diedrich in #85
• Unify anndata handling 7 | alphatools.pp.impute_median by @lucas-diedrich in #101
• Data Module by @lucas-diedrich in #104
• Unify anndata handling 8 | alphatools.metrics.pooled_median_absolute_deviation by @lucas-diedrich in #108
• New remove redundancy by @shanibmo in #112
• [API] Rename alphatools → alphapepttools by @lucas-diedrich in #115

Bug fixes

• [Fix] Fix warning message in PSM reader and check per sample/run by @lucas-diedrich in #37
• [Bugfix] fixing a subtle mistake in get_color_mapping in colors(), and the associated _get_colors_from_cmap() by @vbrennsteiner in #45
• Handling of nan values in normalization by @lucas-diedrich in #55
• [Fix] Clamp explained variance in PCR at 0 by @lucas-diedrich in #96
• [Test] Fix flaky test by @lucas-diedrich in #105

New Features

• [Feature] Principal Component Regression by @lucas-diedrich in #25
• Pooled Median Absolute Deviation by @lucas-diedrich in #27
• Median normalization by @lucas-diedrich in #56
• PSM table reader function by @lucas-diedrich in #54
• Protein Group Reader by @lucas-diedrich in #52
• AlphaQuant Differential expression by @vbrennsteiner in #73
• Median imputation by @lucas-diedrich in #82
• KNN imputation by @lucas-diedrich in #103
• Anndata Factory Capabilities by @vbrennsteiner in #99

Other Changes / unlabeled

• setting up repo from scverse template by @mschwoer in #1
• Additions to template by @mschwoer in #2
• Update README.md by @JuliaS92 in #3
• Add code review action by @mschwoer in #4
• Basic data handling by @vbrennsteiner in #5
• Adding metadata filtering functionality via "filter_by_metadata()" by @vbrennsteiner in #7
• Basic histogram & completeness filtering (+ plotting infrastructure to get there) by @vbrennsteiner in #6
• Add new dataset by @mschwoer in #9
• Add anndata factory by @mschwoer in #11
• Rank plot by @shanibmo in #13
• Basic scatter by @vbrennsteiner in #14
• Strip nb metadata by @mschwoer in #12
• Add logo draft by @lucas-diedrich in #17
• Adding PCA preprocessing functions by @shanibmo in #16
• Notebooks to tutorials by @lucas-diedrich in #21
• Gaussian imputation by @vbrennsteiner in #31
• Total Mean normalization by @lucas-diedrich in #30
• [Docs] Include all existing modules in the docs by @lucas-diedrich in #24
• Filter completeness groupwise by @vbrennsteiner in #26
• Add functions to map protein groups to genes by @vbrennsteiner in #23
• remove the notebooks folder by @mschwoer in #33
• PCA related plots by @shanibmo in #29
• Legend from dict by @vbrennsteiner in #20
• Fix bug in data.py/add_metadata by @vbrennsteiner in #10
• Log transform by @vbrennsteiner in #18
• Fix coloring bug by @vbrennsteiner in #36
• add comment to better understand current and future state of the anndata factory. by @vbrennsteiner in #38
• Add option to enumerate axes in publication style, e.g. A, B, C, etc … by @vbrennsteiner in #40
• Modify PCA and related plotting functions to run on feature dimension by @shanibmo in #35
• [nit] add default argument for colormap by @vbrennsteiner in #44
• [nit] switch to more robust nan check in _drop_nans_from_plot_arrays by @vbrennsteiner in #43
• Mapped color shapes by @vbrennsteiner in #42
• Add release workflows by @mschwoer in #47
• Add release workflows by @mschwoer in #48
• fix return type of color palette maker to return a list of rgba tuples by @vbrennsteiner in #50
• revert change of return type of _get_colors_from_cmap back to cmpa(va… by @vbrennsteiner in #51
• [enhancement] Simplify labelling by @vbrennsteiner in #46
• separated the PCA plotting functions from the data handling functions by @shanibmo in #49
• new alphabase version 1.7.1 with fix for datashare by @vbrennsteiner in #65
• Enh color mapping track for plots by @vbrennsteiner in #53
• Example notebook by @vbrennsteiner in #39
• update URLs in notebooks and tests to reflect new data share links by @mschwoer in #63
• Pycombat scanpy by @vbrennsteiner in #41
• rewrite plot labelling test to be rank based by @vbrennsteiner in #69
• [Fix] Fix API documentation - Expose read_pg_table to users by @lucas-diedrich in #70
• Differential expression by @vbrennsteiner in #72
• Grouped quantity plot by @vbrennsteiner in #71
• switch alphatools default color palette to rearranged bartlow and update notebooks by @vbrennsteiner in #74
• Fix empty pg index by @vbrennsteiner in #75
• Design guidelines in readme by @vbrennsteiner in #77
• Nb data sources update by @lucas-diedrich in #78
• Nb data sources by @vbrennsteiner in #76
• Update and prettify the Plotting notebook by @vbrennsteiner in #79
• use fixed bin range for multi-level histograms to avoid different bin… by @vbrennsteiner in #81
• the previous test for plot labelling checked for identical row order … by @vbrennsteiner in #80
• [CI/CD] Build docs in private location by @lucas-diedrich in #94
• Add UMAP functionality in 04 notebook by @shanibmo in #60
• fix bug in notebook 01 where accidentally the nans were counted inste… by @vbrennsteiner in #97
• Unified layer handling 1 | Formalize unified layer + anndata handling in alphatools in documentation by @lucas-diedrich in #84
• Pycombat metrics tutorial by @lucas-diedrich in #83
• Refactor imputation test by @lucas-diedrich in #102
• Remove legacy functions by @lucas-diedrich in #100
• harmonize pca_plot interface to follow the convention of scatter by @vbrennsteiner in #66
• Basic analysis notebook by @vbrennsteiner in #87
• Empirical Bayes moderated t-test by @vbrennsteiner in #106
• [Refactor] anndata factory by @lucas-diedrich in #111
• make build_wheel.sh executable by @mschwoer in #116
• CITATION.cff by @lucas-diedrich in #117
• [Fix] Update src_folder path in publish_on_pypi.yml by @mschwoer in #118
• [VERSION] Bump version to 0.0.1 by @github-actions[bot] in #119

New Contributors

• @JuliaS92 made their first contribution in #3
• @vbrennsteiner made their first contribution in #5
• @shanibmo made their first contribution in #13
• @lucas-diedrich made their first contribution in #17

Full Changelog: https://github.com/MannLabs/alphapepttools/commits/v0.0.1