Differential Analysis
=====================

Input
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- Count matrix (genes or pathways)
- Sample metadata

Model
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Use designs such as:

.. code-block:: R

   ~ condition + batch

Tools
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- DESeq2 (RNA-seq style count data)
- edgeR
- Limma-Voom

Visualizations
--------------

- Volcano plots
- Heatmaps
- PCA / ordination