seurat

Version:: 4.4
Category:: bio
Cluster:: Loki

Author / Distributor

https://satijalab.org/seurat/articles/get_started_v5_new

Description

Seurat (Satija Lab) is a unified, high-level framework for single-cell transcriptomics, multimodal data (e.g., RNA + ATAC), and spatial transcriptomics. It has a large user base and extensive documentation, making it an excellent starting point for new analysts.

Seurat v5 introduced a layered assay structure and improved support for large-scale datasets, including disk-backed matrices and sketch-based workflows for million-cell analyses. The ecosystem also supports reference mapping (e.g., Azimuth) and integrates well with multimodal workflows.

Documentation

[options]

Examples/Usage

List available modules:
```
$ module avail seurat
```
Load the samtools module:
```
$ module load
```
Check the loaded modules:
```
$ module list
```
Unload the samtools module:
```
$ module unload bio/SAMtools/1.15.1
```
create a sequence dictionary file:
```
$ samtools dict
```
quickly check if SAM/BAM/CRAM file appears intact:
```
$ samtools quickcheck
```

Installation

Source code is obtained from Seurat