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- Analyzing single-cell regulatory chromatin in R. • ArchR
ArchR provides the most extensive suite of scATAC-seq analysis tools of any software available Additionally, ArchR excels in both speed and resource usage, making it possible to analyze 1 million cells in 8 hours on a MacBook Pro laptop To get started, we recommend running through the brief ArchR tutorial
- GreenleafLab ArchR: ArchR - GitHub
ArchR is currently in Beta and will be in active development through the peer review process ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data ArchR provides the most extensive suite of scATAC-seq analysis tools of any software available
- ArchR: Robust and scaleable analysis of single-cell chromatin . . .
ArchR: Robust and scaleable analysis of single-cell chromatin accessibility data ArchR is a full-featured software suite for the analysis of single-cell chromatin accessibility data
- GitHub - swaruplabUCI ArchRtoSignac: An R package performing object . . .
ArchRtoSignac is an R package to convert an ArchRProject (ArchR) to a Signac SeuratObject (Signac) ArchR and Signac are both commonly used scATAC-seq analysis packages with comparable sets of features and are currently under development, which means they are likely to change over time
- Chapter 3 Getting Started with ArchR | ArchR: Robust and scaleable . . .
1Debugging and Troubleshooting in ArchR 2Manage ArchR’s Dependencies 2 1Using renv to manage dependencies 2 2Other environment managers 2 3Using Docker for pre-compiled environment setup 3Getting Started with ArchR 3 1A Brief Primer on ATAC-seq Terminology 3 2Why use ArchR? 3 3What is an Arrow file ArchRProject?
- A Brief Tutorial of ArchR
Importantly, this tutorial and the full user manual assume that you are running ArchR locally First, we load the ArchR library If this fails, you have not properly installed ArchR and should revisit the installation instructions
- 9. 1 Calculating Gene Scores in ArchR | ArchR: Robust and scaleable . . .
9 1 Calculating Gene Scores in ArchR | ArchR: Robust and scaleable analysis of single-cell chromatin accessibility data In our publication, we tested over 50 different gene score models and identified a class of models that consistently outperformed the rest across a variety of test conditions
- Chapter 6 Dimensionality Reduction with ArchR | ArchR: Robust and . . .
In ArchR, these visualization methods are referred to as embeddings
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