# ATAC-seq

```{toctree}
:maxdepth: 1

notebooks/atac/PeakVI
notebooks/atac/PoissonVI
notebooks/atac/scbasset
notebooks/atac/scbasset_batch
```

```{customcard}
:path: notebooks/atac/PeakVI
:tags: Analysis, Differential-comparison

Go through the PeakVI workflow to analyze a scATAC-seq dataset
```

```{customcard}
:path: notebooks/atac/PoissonVI
:tags: Analysis, Differential-comparison

Go through the PoissonVI workflow to analyze scATAC-seq data using quantitative fragment counts
```

```{customcard}
:path: notebooks/atac/scbasset
:tags: Analysis, Integration

Go through the scBasset workflow to analyze a scATAC-seq dataset
```

```{customcard}
:path: notebooks/atac/scbasset_batch
:tags: Integration, Dimensionality-reduction, Removal-of-variance

Use scBasset to integrate data across several samples
```