Release notes


Bug fixes

  • read_gmt is now properly exported.


Bug fixes

  • plot_metrics_scatter_cols now deals with missing sources when comparing nets.


  • get_pseudobulk and get_acts now have a dtype argument due to future AnnData changes.

  • plot_metrics_scatter and plot_metrics_boxplot now use GroupBy.mean(numeric_only=True).


  • Added swap_layer function to easily move adata layers to .X.

  • Added read_gmt function to read GMT files containing gene sets.



  • Omnipath wrappers (get_resource, get_dorothea and get_progeny) now accept any organism name.


Bug fixes

  • Fixed change in api from sklearn.tree.

  • Forced gene names in extract to be in unicode format.

  • Changed integer format from int32 to int64 to accommodate larger datasets across methods.


  • Added conversion utility function translate_net to translate nets across organisms.


Bug fixes

  • Removed python <3.10 limitation.

  • Forced np.float32 type to output of get_contrast.

  • Made summarize_acts compatible with older versions of numpy.

  • extract_psbulk_inputs now checks if mat and obs have matching indexes.

  • plot_volcano now correctly can plot networks with different source names.


  • extract now removes empty samples and features.

  • run_consensus now follows the same format as other methods, old function is now called cons.

  • get_pseudobulk now checks if input are raw integer counts.

  • plot_volcano now can plot without subsetting features by a network and can save plots to disk.

  • plot_volcano now uses adjustText to better plot text labels.

  • plot_volcano now can set logFCs and p-value limits for outliers.

  • get_top_targets now can also work without subsetting features by a network and returns significant adjusted p-values.

  • get_contrast now can also work without needing to group.

  • udt and mdt now check if skranger and sklearn are installed, respectively.

  • get_toy_data now contains more example TFs.

  • get_top_targets now returns logFCs and pvals as column names instead of logFC and pval.

  • format_contrast_results now returns also the adjusted p-value.


  • Added dense_run util function which runs methods ignoring zeros in the data.

  • Added plot_violins and plot_barplot functions.

  • Added p_adjust_fdr util function to correct p-values for FDR.

  • Added get_ora_df function to infer ora from lists of genes instead of an input mat.

  • Added shuffle_net function to randomize networks.

  • Added benchmarking metrics metric_auroc, metric_auprc, metric_mcauroc and metric_mcauprc.

  • Added get_toy_benchmark_data function to generate a toy example for benchmarking.

  • Added show_metrics function to show available metrics.

  • Added benchmark, format_benchmark_inputs and get_performances functions to benchmark methods and nets.

  • Added plot_metrics_scatter function to plot the results of running the benchmarking pipeline.

  • Added plot_metrics_scatter_cols function to plot the results of running the benchmarking pipeline grouped by two levels.

  • Added plot_metrics_scatter function to plot the results of running the benchmarking pipeline.

  • Added plot_metrics_boxplot function to plot the distributions of Monte-Carlo benchmarking metrics.


Bug fixes

  • Fixed get_pseudobulk errors.

  • Fixed get_progeny to correctly return non duplicate entries.

  • Fixed run_viper parallelization error.

  • Fixed run_ora to correctly deal with random ties.


  • get_dorothea now returns an ordered dataframe.

  • get_contrast now prints warnings instead of returning an empty dataframe.


  • Added get_top_targets util function.

  • Added format_contrast_results util function.