In ycl6/scRUtils: Single-Cell Sequencing Analysis Utilities

knitr::opts_chunk$set(error = FALSE, warning = FALSE, message = TRUE, tidy = FALSE, 
              cache = FALSE, dpi = 100)
library(BiocStyle)
library(DESeq2)

Overview

scRUtils provides various utilities for visualising and functional analysis of RNA-seq data, particularly single-cell dataset. It evolved from a collection of helper functions that were used in our in-house scRNA-seq processing workflow.

The documentation of this package is divided into 5 sections:

1. Introduction to scRUtils
2. General data visualisations
3. Single-cell visualisations
4. Markers and DEGs
5. Demo datasets

This vignette (#1) will introduce the package and the included demo datasets.

Installation

The package is current available only on GitHub.

devtools::install_github("ycl6/scRUtils")

Load packages

To use scRUtils in a R session, load it using the library() command.

library(scRUtils)

Use demo datasets

Demo datasets were created to demonstrate functions available in this package. The datasets can be loaded by using data(). Details on how the datasets were produced can be found in the following vignette: Creating demo datasets.

cyclone result

phases_assignments is a list object of 3, containing cyclone results performed on a simulated scRNA-seq dataset.

data(phases_assignments)
str(phases_assignments)

table(phases_assignments[["phases"]])

findDoubletClusters result

dbl_results is a DFrame object containingfindDoubletClusters results performed on a simulated scRNA-seq dataset.

data(dbl_results)
dbl_results

Processed simulated single-cell RNA-seq dataset

sce is a SingleCellExperiment object that has been processed with additional information stored.

data(sce)
sce

# rowData
rowData(sce)

# colData
colData(sce)

# metadata
names(metadata(sce))

edgeR's TopTags object

res_edger is a TopTags object containing differential expression analysis results of the pasilla dataset.

data(res_edger)
DataFrame(res_edger)

DESeq2's DESeqResults object

res_deseq2 is a DESeqResults object containing differential expression analysis results of the pasilla dataset.

data(res_deseq2)
DataFrame(res_deseq2)

Session information {-}

sessionInfo()

ycl6/scRUtils documentation built on Feb. 18, 2025, 6:14 a.m.