Overview
DOtools is a user-friendly R package designed to streamline common workflows in single-cell RNA sequencing (scRNA-seq) data analysis using the Seurat ecosystem and third-party tools such as scVI, CellTypist, and CellBender. It provides high-level wrappers and visualisation utilities to help efficiently preprocess, analyze, and interpret single-cell data.
Installation
DOtools is currently available through Bioconductor. To install the package, start R and run:
install.packages("BiocManager")
BiocManager::install("DOtools")Requirements
Some functions in this package depend on Python packages or scripts. These functions use basilisk to create isolated environments, which are built using conda. As a result, a working conda installation is required. The DoTools pipeline was tested on Linux and MacOS and an example dataset with ~65k cells can be processed with a machine with at least 16GBs of RAM memomy and 5 CPUs.
Python package
If you prefer python over R for data analysis, we also provide a python version of the DOtools package. Please refer for the python version to: DOtools_py
Contribution Guidelines
Raising up an issue in this Github repository might be the fastest way of submitting suggestions and bugs. Alternatively you can write an email: ruzjurado@med.uni-frankfurt.de