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Update DESeq2.md
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siebrenf authored Sep 13, 2023
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Alternatively, you can call the DESeq2 script from the command line.
To get started with the command line script, try out `deseq2science --help`.

This section details how the contrast designs are created.
This page details how the contrast designs are created.
Examples are given [below](./DESeq2.html#contrast-designs), and each `config.yaml` contains a commented-out example contrast design at the bottom.

##### single-cell DESeq2
If your counts table contains all cells, and your samples.tsv contains a group identifier for each cell, you can perform DESeq2 on this data using `deseq2science` by passing the `--single-cell` flag.
Please note that `deseq2science` can accept a gzipped tsv file as well.

Also note that the `--single-cell` flag should *not* be used with pseudo-bulk.
Also note that the `--single-cell` flag should *not* be used with pseudo-bulk counts.

##### Overview of the DESeq2 method
DESeq2 automatically performs library bias correction when loading your data, and batch correction is performed if it is included in the contrast design.
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