README.md

In tanaylab/repsc: Single-cell expression analysis of transposable elements

Important: this package is not maintained anymore

Repsc

The Repsc R package is a beta development version to facilitate expression analysis of transposable elements at single-cell resolution.

Functionality

The basic workflow consists of importing genome annotation/sequencing reads, curating TE and gene intervals, counting overlaps, and generating the single-cell matrix. Repsc supports a wide range of protocols, including 5’/3’ and full-coverage based methods, but for unambiguous assignment of reads to de-repressed TE loci we recommend 5’ based protocols:

Features include:

• Multi-species support
• Flexible genome annotation
• Gene and TE curation
• 5’/3’/full-coverage support
• High-quality reports

More details on the usage of Repsc is available in the package vignette.

Installation

# Install BiocManager (in case you haven't already)
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# Install Remotes (in case you haven't already)
if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")

# Install Repsc
remotes::install_github('tanaylab/repsc')

Note: Repsc requires R version 3.5 or higher. The package was tested on linux. We are working on reducing memory usage, but currently a typical application will require at least 12 GB RAM, but heavier use cases (e.g. large BAM files) may require significantly more. For improved speed performance, we recommend a multi-CPU/core workstation, or ideally a HPC infrastructure.

tanaylab/repsc documentation built on Jan. 9, 2021, 9:39 a.m.