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Recent Releases of alphastats

alphastats - v0.7.1

What's Changed

Other Changes / unlabeled

  • Make create id dicts static by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/453
  • Allow custom analysis by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/452
  • Refactor results by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/455
  • Fixes for some tickets by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/458
  • Add custom upload by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/456
  • Hotfixes by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/464
  • Fix docs by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/469

Full Changelog: https://github.com/MannLabs/alphapeptstats/compare/v0.7.0...v0.7.1

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Published by github-actions[bot] 11 months ago

alphastats - v0.7.0

Major improvements / New Features

  • Validation and refactoring of differential expression analysis by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/388
  • 0 value handling by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/345
  • UI code refactoring up to analysis by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/304
  • Live representation of selected steps in predefined workflow by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/308
  • New backend for results display and interface for volcano plot by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/390
  • Save sessions by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/403

Improvements

  • TODO on tqdm to streamlit by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/302
  • Basic tests for page 2 and 3 by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/305
  • Testpage3 by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/310
  • Tests page 3 by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/319
  • Enable multicova by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/347
  • Add type based string representation of artifacts by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/404
  • Gprofiler, but also more String changes by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/414
  • speed up sam test by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/420
  • switch double bookkeeping to namedtuple by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/423
  • Switch to Pyproject.toml by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/433
  • Hide old dea by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/440
  • Rerenable docker by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/438
  • Major refactoring by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/441

Technical (reformatting, linting)

  • Sync developement with main by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/279
  • sync dev with main by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/281
  • #276: apply pre-commit end-of-file-fixer, trailing-whitespace, check… by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/282
  • #276: apply pre-commit ruff-format by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/283
  • 276 formatting by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/287
  • #276: add pre-commit to CI by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/284
  • bump dev to 0.6.7 by @boopthesnoot in https://github.com/MannLabs/alphapeptstats/pull/288
  • refactoring_import by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/306
  • Refactoring import ii by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/307
  • Bump streamlit by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/309
  • Adapt to new release workflow by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/303
  • disable caching by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/314
  • remove double imports by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/315
  • add detect-secrets pre-commit hook by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/318
  • add code review action by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/321
  • Add fix imports by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/327
  • String constants session state by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/326
  • Draft refactor dataset by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/322
  • Introduce string constants by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/324
  • move initialization of preprocessing to Preprocess, change initializa… by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/325
  • Decouple dataset from enrichment by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/328
  • Decouple dataset from statistics by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/329
  • Decouple dataset from plots by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/332
  • simplify-dataset-init by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/333
  • Linitin rule i by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/334
  • Linitin rule sim by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/335
  • rename metadatapath -> metadatapathordf by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/336
  • linitingruleB by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/348
  • linitingruleF by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/349
  • linitingruleE by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/350
  • simplify_analysis-II by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/351
  • simplify_analysis-III by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/352
  • Remove index column by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/362
  • Remove gene names column by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/363
  • Remove sample column by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/364
  • Refactor analysis i by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/366
  • Refactor analysis ii by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/367
  • Refactor analysis iii by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/368
  • Refactor analysis iv by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/369
  • Refactor analysis v by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/370
  • Refactor analysis vi by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/371
  • Refactor analysis vii by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/372
  • Refactor analysis viii by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/373
  • add changes/comments requested by code review by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/374
  • Rename modules by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/375
  • remove duplicated test files by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/377
  • add stricter linting by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/391
  • add code review by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/392
  • main -> development by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/394
  • move session state keys to dedicated module by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/402
  • add version to pickle by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/405
  • Small improvements by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/406
  • ruff by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/415
  • UI improvements by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/410
  • UI improvements ii by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/416
  • Bumpversion by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/437
  • Use latest streamlit by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/436
  • [VERSION] Bump version to 0.7.0 by @github-actions in https://github.com/MannLabs/alphapeptstats/pull/444

Bug fixes

  • Annotation retrieval and textualization by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/383
  • Idhandling ii by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/379
  • Idhandling I by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/378
  • Add download button to get chatlog. by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/387

  • dynamically choosing proteins from volcano plot by @boopthesnoot in https://github.com/MannLabs/alphapeptstats/pull/389

  • FIX: corrupted excel metadata template by @boopthesnoot in https://github.com/MannLabs/alphapeptstats/pull/290

  • Fix tests by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/294

  • Fix app by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/312

  • Redo hotfixes clean by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/313

  • Init session state everywhere by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/316

  • fix a method call by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/317

  • fix merge conflicts by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/331

  • Logfix by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/340

  • Fix if condition dev by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/343

  • fix plotting by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/376

  • Fix metadata template by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/401

  • Fix intensity plot by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/417

  • UI improvements and model loading fix by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/419

  • Hotfixes by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/424

  • fix: technical message showed in the chat by @boopthesnoot in https://github.com/MannLabs/alphapeptstats/pull/435

  • Fix pickle by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/428

  • Client setting on load slightly adjusted by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/442

New Contributors

  • @PatriciaSkowronek made their first contribution in https://github.com/MannLabs/alphapeptstats/pull/422
  • @github-actions made their first contribution in https://github.com/MannLabs/alphapeptstats/pull/444

Full Changelog: https://github.com/MannLabs/alphapeptstats/compare/v0.6.9...v0.7.0

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Published by github-actions[bot] about 1 year ago

alphastats - Release v0.6.9

What's Changed

  • Fix wrong if condition by @mschwoer in https://github.com/MannLabs/alphapeptstats/pull/341

Full Changelog: https://github.com/MannLabs/alphapeptstats/compare/v0.6.8...v0.6.9

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Published by github-actions[bot] almost 2 years ago

alphastats - Release v0.6.8

What's Changed

  • BUGFIX: remove additions before log transform by @JuliaS92 in https://github.com/MannLabs/alphapeptstats/pull/337
  • FIX: corrupted excel metadata template by @boopthesnoot in https://github.com/MannLabs/alphapeptstats/pull/289

Full Changelog: https://github.com/MannLabs/alphapeptstats/compare/0.6.7...v0.6.8

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Published by github-actions[bot] almost 2 years ago

alphastats - Release 0.6.7

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Published by github-actions[bot] about 2 years ago

alphastats - Release alphastats_0.6.6

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alphastats - Release alphastats_0.6.5

- Jupyter Notebook
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alphastats - Release alphastats_0.6.4

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alphastats - Release alphastats_0.6.3

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alphastats - Release alphastats_0.6.2

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alphastats - Release alphastats_0.6.0

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alphastats - Release alphastats_0.5.4

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alphastats - Release alphastats_0.5.3

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alphastats - Release alphastats_0.5.2

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alphastats - Release alphastats_0.5.1

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alphastats - Release alphastats_0.5.0

  • ADD plot Sample Distribution Histogram
  • ADD paired-ttest option
  • ENH add option to remove samples in GUI
  • ADD pyComBat Batch correction Behdenna A, Haziza J, Azencot CA and Nordor A. (2020) pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods. bioRxiv doi: 10.1101/2020.03.17.995431
  • ENH remove iteration utilities, remove C++ dependency
  • ENH upgrade to pandas 2.0.0

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Published by github-actions[bot] about 3 years ago

alphastats - Release alphastats_0.4.5

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Published by github-actions[bot] over 3 years ago

alphastats - Release alphastats_0.4.4_fix

Fix one-clickinstaller issues

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alphastats - Release alphastats_0.4.3

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alphastats - Release alphastats_0.4.2

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alphastats - Release alphastats_0.4.1

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alphastats - Release 0.4.0

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alphastats - Release alphastats_0.3.0

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alphastats - alphastats_v0.2.7

  • Fix warning when loading DIA-NN GUI

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Published by elena-krismer over 3 years ago

alphastats - alphastats_v0.2.6

  • Bug fix when importing data in GUI
  • version binning

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Published by elena-krismer over 3 years ago

alphastats - alphastats_v0.2.5

  • DataSet overview tab
  • allow download of data matrix in GUI

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Published by elena-krismer over 3 years ago

alphastats - alphastats_v0.2.4

0.2.4

  • added kaleido dependency
  • GUI add button to reset preprocessing
  • GUI combine visualization and analysis
  • Display seaborn clustermap in GUI
  • GUI fixes

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Published by elena-krismer over 3 years ago

alphastats - alphastats_v0.2.3

  • fix umap import
  • version report in GUI
  • Bug fix GUI

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Published by elena-krismer over 3 years ago

alphastats - alphastats_v0.2.2

  • rename AlphaStats to AlphaPeptStats
  • GUI bug fixes

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Published by elena-krismer over 3 years ago

alphastats - alphastats_v0.2.1

*fix requirements *function renaming performdiffexpranalysis > performdiffexpranalysis, calculatetukey -> tukeytest

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Published by elena-krismer over 3 years ago

alphastats - alphastats_v0.2.0

  • Gene Ontology Enrichment Analysis using a GO tool

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Published by elena-krismer over 3 years ago

alphastats - alphastats_v0.1.2

  • rawdata renamed to rawinput
  • bug fix in GUI

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Published by elena-krismer over 3 years ago

alphastats - alphastats_v0.1.1

  • Graphical User Interface
  • Volcano Plot can be plotted with cut off lines, add labels to significant enriched proteins
  • plot-intensity with t-test between two groups
  • Differential Expression analysis + Volcano Plot can be calcultated/plotted with list of sample names
  • UMAP

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Published by elena-krismer over 3 years ago