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v0.5.0

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@katosh katosh released this 06 Oct 17:51
· 92 commits to main since this release
  • comprehensive FDR implementation for differential expression analysis
  • FDR-based visualization in volcano_de plots: support for local/tail FDR y-axes and coloring
  • posterior tail probability for differential expression
  • introduction of "is_de" boolean column in adata.var to indicate differential expression based on significance threshold
  • more flexible volcano_de plot with FDR/PTP-based thresholding and y-axis options
  • "signal" and "strength" columns in stringDB gene-set enrichment analysis
  • expand testing
  • rename fields to include comparison, e.g., "A_to_B", before statistic name
  • make de significance measures tail fdr, ptp, and zscore optional
  • implement cleanup function
  • bugfix: Prevent silent failure of compute_differential_abundance with sample variance
    by making sure enough space is available on disk for covariance tensor.
  • dry run for differential expression
  • split tutorials in 3 parts
  • reduce memory demand when using batching and reflect this in dry run
  • fix disk space checking to respect TMPDIR environment variable consistently
  • include all computed results in full results dictionaries (std, fiel names, etc.)