Catullus

A collection of useful functions for scRNA-seq analysis, meant to be utilized with tiledbsoma experiment objects.

Installation

The package requires the tiledbsoma package be installed. See this repository for details on this installation. Once this dependency is installed, one can install Catullus as follows:

remotes::install_github("ccnawrocki/Catullus")

Usage

There are three function types in Catullus: Do, View, and Get.

• A Do function performs an operation or test.
• A View function creates a plot.
• A Get function simply retrieves something for future use.

Reference

Here is a list of all the functions included in Catullus:

DoDETesting
DoPseudobulkAggregation
ViewDETesting
ViewMeta
ViewExpression
GetDEData
GetObjectSchema
GetGeneData
GetCellGroupIDs
GetDimRedData
GetMetaData
GetExpressionData

Quickstart Vignette

The following vignette uses a subset of the data from Briggs et al. 2018.

First, open the tiledbsoma experiment object and check the schema.

library(Catullus)
experiment <- tiledbsoma::SOMAExperimentOpen("briggs_data_stage22_SOMA")
GetObjectSchema(experiment)

Examining the schema (not shown), we see that louvain clustering was performed on this data and that the results are saved in the metadata in the "louvain_33_clusters" column. Let's look at the UMAP, labeling the clusters.

Catullus::ViewMeta(exp_object = experiment, color_var = "louvain_33_clusters", labeling = T, legend = F)

Now, let's look again at the UMAP, but let's see which clusters express a known gene of interest, pax6.

Catullus::ViewExpression(exp_object = experiment, genes = "pax6", label_var = "louvain_33_clusters")