In FelixTheStudent/scUtils: Utility Functions for Single-Cell RNA Sequencing Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

scUtils

The goal of scUtils is to collect utility functions that make single-cell RNAseq data analysis simple and understandable for anyone. At the same time, I will use it when writing my PhD thesis.

Installation

You can install the released version of scUtils from CRAN with:

install.packages("scUtils")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("FelixTheStudent/scUtils")

Example: Single-Cell Feature Plot

Feature Plots highlight gene expression in a 2-dimensional embedding (computed e.g. with UMAP or tSNE).

library(scUtils)

# simulate some data
set.seed(100)
my_umap <- matrix(rnorm(2000, c(.1, 3)), ncol=2, dimnames = list(NULL, c("umap_1", "umap_2")))
my_expr <- rpois(1000, c(.1, 11))

feat(my_umap, my_expr)