Overview

Utopian data structure

Panopticon is a set of tools named after Jeremy Bentham’s model for a prison, whereby multiple cells (!) could be observed with ease by a single individual.

This package is designed to provide functionality I didn’t find in other general single-cell RNA analysis tools, such as Seurat and scanpy.

A few unique features include

  • functions for joint analysis of bulk DNA and single-cell RNA

  • functionality for processing of CITE-seq/feature barcoding, as well as guide RNAs (for perturb-Seq)

  • functions for analyzing single cell TCR-seq data

  • out-of-memory operation (due to the reliance on loom files)

  • convenient iterative subclustering (by default agglomerative clustering with a Pearson correlation or cosine metric, with number of clusters selected by silhouette score)

Panopticon relies on loom files with certain demands on column and row attributes. These follow the spirit of the Linnarsson lab style guide, albeit with some different choices. For details please see the Panopticon Style Guide.