scRUtils: Single-Cell Sequencing Analysis Utilities

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.

Installation

First, install Bioconductor packages that scRUtils depends on in a conda environment or in R using the BiocManager::install function.

conda install -c bioconda bioconductor-scuttle bioconductor-scater bioconductor-complexheatmap \
bioconductor-bluster bioconductor-summarizedexperiment bioconductor-singlecellexperiment bioconductor-s4vectors

BiocManager::install(c("scuttle","scater","ComplexHeatmap","bluster","SummarizedExperiment",
                       "SingleCellExperiment","S4Vectors"))

The package is current available only on GitHub, so please use devtools::install_github or remotes::install_github function to install it.

devtools::install_github("ycl6/scRUtils")

Load packages

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

library(scRUtils)

Usage

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

Contributing

Thank you for investing your time in contributing to scRUtils. You will get an overview of the contribution workflow in this dedicated guide. By contributing to this project, you agree to abide by the terms outlined in the Contributor Code of Conduct.