The goal of posDemux is to provide tools for tools for handling reads with combinatorial barcodes, and multiple adapter regions. This includes utilities for demultiplexing, sequence segmenting and filtering. The package is intended to work with single-cell RNA-seq data with multiple barcoding (e.g. SPLiT-seq and PETRI-seq).
Installation
As of release 3.23, the package is hosted on the Bioconductor repository for R packages. In order to install it from a fresh R install, run:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("posDemux")
## Check that you have a valid Bioconductor installation
BiocManager::valid()If you want to obtain the development version of the package, it is available on GitHub:
if (!requireNamespace("devtools", quietly = TRUE)) {
install.packages("devtools")
}
devtools::install("yaccos/posDemux")If you compile the package from source, we do recommend you use the compiler flag -ftree-vectorize as this provides considerable speedup to the demultiplexer.
Usage
Please see the package vignettes.