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Changelog

0.6.6

  • FIX preprocessing with 0 / NA discrepancy

0.6.5

  • FIX coloring of plot_sampledistribution issue #229
  • ADD nbformat requirement issue #230

0.6.4

  • FIX windows installer

0.6.3

  • ENH download metadata template in the GUI
  • ENH multicova analysis
  • ENH filter data completeness dataset.preprocess(data_completeness=0.7)
  • ADD GenericLoader for not supported data formats

0.6.2

  • FIX preprocessing with VST floats and inf
  • FIX plotly display

0.6.1

  • FIX data loading

0.6.0

  • ADD mzTAB support
  • ENH color Volcano Plot data points using list of protein names color_list=your_protein_list

0.5.4

  • FIX altair version - binning of streamlit version

0.5.3

  • FIX FragPipe loading issue

# 0.5.2

  • FIX FragPipe import #173

0.5.1

  • ENH increase limit uplaod size in GUI

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
  • remove iteration utilities, remove C++ dependency
  • ENH upgrade to pandas 2.0.0

0.4.5

  • FIX loading of Data on Windows

0.4.4

  • FIX one click installer

0.4.3

  • FIX loading dataset with columns
  • ADD log2-transformation

0.4.2

  • ADD option compare_preprocessing_modes
  • update to streamlit 1.19 with new caching functions

0.4.1

  • FIX bug when drawing FDR lines
  • ADD functionionality dataset.reset_preprocessing() to reset all preprocessing steps

0.4.0

  • SAM implementation from Isabel (MultiCova)
  • Volcano Plot with permutation based FDR line
  • Bug fix when reseting matrix and saving info

0.3.0

  • One Click Installer for macOS, Linux and Windows
  • Spectronaut support

0.2.8

  • enhance performance of plotting VolanoPlots in the GUI
  • refactoring of plotting classes
  • BUG fix when importing new dataset in GUI

0.2.7

  • Fix warning when loading DIA-NN GUI

0.2.6

  • Bug fix when importing data in GUI
  • version binning

0.2.5

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

0.2.4

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

0.2.3

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

0.2.2

  • rename AlphaStats to AlphaPeptStats
  • GUI bug fix

0.2.1

  • fix requirements
  • function renaming perform_diff_expr_analysis > perform_diff_expr_analysis, calculate_tukey -> tukey_test

0.2.0

  • Gene Ontology Enrichment Analysis using a GO tool

0.1.2

  • rawdata renamed to rawinput
  • GUI bug fix

0.1.1

  • 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

0.0.6

  • remove dependency for Microsoft Visual Studio C++ (dash_bio) (Windows PCs)
  • clustermap with seaborn, adding bar labels is possible
  • save plotting data, preprocessing, method in figure object (accessible using figure.plotting_data, figure.method, figure.preprocessing)