> For the complete documentation index, see [llms.txt](https://documentation.panomics.bio/documentation/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/sample-cell-explorer.md).

# Sample/Cell Explorer

The Explorer modules enable the user to perform deep exploration of the dataset.

<figure><img src="https://3894776587-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FUZMYHWMJyvkxhr9s6Lm5%2Fuploads%2FdOSjONAOEvewRMa48lA2%2FScreenshot%202024-10-24%20at%2016.52.45.png?alt=media&amp;token=e722a8c4-602e-48a5-bbf6-b761ecf3b702" alt=""><figcaption><p>Sample/Cell Explorer</p></figcaption></figure>

## Available commands

<table data-view="cards"><thead><tr><th></th><th></th><th></th><th data-hidden data-card-target data-type="content-ref"></th></tr></thead><tbody><tr><td></td><td><strong>Normalization</strong></td><td>Normalize the expression data.</td><td><a href="/documentation/analyses/analysis-workbench/sample-cell-explorer/normalization.md">Normalization</a></td></tr><tr><td></td><td><strong>UMAP</strong></td><td>Compute PCA, neighborhood graph, UMAP, and eliminate batch effects.</td><td><a href="/documentation/analyses/analysis-workbench/sample-cell-explorer/umap.md">UMAP</a></td></tr><tr><td></td><td><strong>Clustering</strong></td><td>Cluster the cells or samples.</td><td></td></tr><tr><td><strong>Differential Gene Expression</strong></td><td>Quickly run differential gene expression analysis between selected groups.</td><td></td><td></td></tr><tr><td><strong>Pathway Activity Inference</strong></td><td>Run pathway activity inference using the gene set collection of choice.</td><td></td><td></td></tr><tr><td><strong>Differential Pathway Activity</strong></td><td>Quickly run differential pathway activity analysis between selected groups.</td><td></td><td></td></tr><tr><td><strong>Remove Cells/Samples</strong></td><td>Delete cell or sample selections.</td><td></td><td></td></tr><tr><td><strong>Filter Cells/Samples</strong></td><td>Isolate cells or samples based on observations.</td><td></td><td></td></tr><tr><td><strong>Plot Gene Expression</strong></td><td>Plot gene expression values or scores.</td><td></td><td></td></tr><tr><td><strong>Plot Pathway Activity</strong></td><td>Plot pathway activity scores.</td><td></td><td></td></tr><tr><td><strong>Annotate Cells/Samples</strong></td><td>Quickly annotate selections</td><td></td><td></td></tr><tr><td><strong>Segment Data</strong></td><td>Create new observations based on other categorical observations.</td><td></td><td></td></tr><tr><td><strong>Remove Observations</strong></td><td>Delete unwanted observations.</td><td></td><td></td></tr></tbody></table>