pylimma
  • Installation
  • Quickstart
  • API reference

Worked examples

  • Differential Expression Analysis of the ALL Chiaretti Microarray Dataset with pylimma
  • Differential Expression Analysis of Mouse Mammary RNA-seq with pylimma
  • Differential Splicing Analysis with pylimma (pasilla dataset)
  • Differential Expression Analysis of Yoruba HapMap RNA-seq with pylimma
  • Single-cell pseudobulk differential expression with pylimma (Kang 2018 PBMC)
  • Differential abundance analysis of proteomics data with pylimma

Validation

  • Parity with R limma
  • Known differences from R limma
  • Fixture-first validation strategy
  • Benchmarks
pylimma
  • Overview: module code

All modules for which code is available

  • pylimma.auroc
  • pylimma.batch
  • pylimma.classes
  • pylimma.contrasts
  • pylimma.decide_tests
  • pylimma.dups
  • pylimma.ebayes
  • pylimma.enrichment
  • pylimma.fitmixture_mod
  • pylimma.genas
  • pylimma.geneset
  • pylimma.lmfit
  • pylimma.normalize
  • pylimma.plotting
  • pylimma.selmod
  • pylimma.splicing
  • pylimma.squeeze_var
  • pylimma.toptable
  • pylimma.utils
  • pylimma.voom
  • pylimma.weights

© Copyright 2026, John Mulvey. Based on R limma by Gordon Smyth et al..

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