> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis.md).

# Differential Analysis

Powerful Partek Flow statistical analysis tools help identify differential expression patterns in the dataset. These can take into account a wide variety of data types and experimental designs.

* [GSA](/partek/partek-flow/user-manual/task-menu/differential-analysis/gsa.md)
* [ANOVA/LIMMA-trend/LIMMA-voom](/partek/partek-flow/user-manual/task-menu/differential-analysis/anova-limma-trend-limma-voom.md)
* [Kruskal-Wallis](/partek/partek-flow/user-manual/task-menu/differential-analysis/kruskal-wallis.md)
* [Detect alt-splicing (ANOVA)](/partek/partek-flow/user-manual/task-menu/differential-analysis/detect-alt-splicing-anova.md)
* [DESeq2(R) vs DESeq2](/partek/partek-flow/user-manual/task-menu/differential-analysis/deseq2-r-vs-deseq2.md)
* [Hurdle model](/partek/partek-flow/user-manual/task-menu/differential-analysis/hurdle-model.md)
* [Compute biomarkers](/partek/partek-flow/user-manual/task-menu/differential-analysis/compute-biomarkers.md)
* [Transcript Expression Analysis - Cuffdiff](/partek/partek-flow/user-manual/task-menu/differential-analysis/transcript-expression-analysis-cuffdiff.md)
* [Troubleshooting](/partek/partek-flow/user-manual/task-menu/differential-analysis/troubleshooting.md)


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