Isosceles

Isosceles (Isoforms from Single-Cell; Long-read Expression Suite) is an R package dedicated to transcript detection and quantification from long reads, supporting both bulk RNA-Seq and scRNA-Seq technologies.

Preprint: https://www.biorxiv.org/content/10.1101/2023.11.30.566884

Installation

Isosceles can be installed using the following commands:

install.packages(c("BiocManager", "devtools"))
BiocManager::install(c("scran", "scater", "uwot", "dittoSeq", "DEXSeq", 
                       "Nebulosa", "ggbio", "BiocStyle"))
devtools::install_github("timbitz/Isosceles", dependencies = TRUE, upgrade = TRUE,
                         INSTALL_opts = "--install-tests")

We found that some versions of Isosceles' dependencies don't work together well, which might cause problems with testing the package or building the vignettes. If you encounter such issues, re-installing certain packages might be helpful:

install.packages("irlba") 
devtools::install_github("powellgenomicslab/Nebulosa", upgrade = FALSE) 

Load the Isosceles package:

library(Isosceles)

Usage

You can follow along with our vignettes (Introduction to the Isosceles package, Mouse E18 brain data analysis) or the reference manual!

Troubleshooting

You can check if the package works correctly by running its unit tests:

testthat::test_package("Isosceles")

In case of any problems, we recommend using the Isosceles Singularity image you can download from Zenodo or installing the package in a Docker container using a Bioconductor image.