Escort is a framework for evaluating a single-cell RNA-seq dataset’s suitability for trajectory inference and for quantifying trajectory properties influenced by analysis decisions. Escort is an R package designed to guide users through the trajectory inference process by offering goodness-of-fit evaluations for embeddings that represent a range of analysis decisions such as feature selection, dimension reduction, and trajectory inference method-specific hyperparameters.
Paper: Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference
Link to Escort website and webserver: https://rbacher.rc.ufl.edu/escort/
You can install Escort via GitHub:
if (!requireNamespace("remotes", quietly=TRUE))
install.packages("remotes")
remotes::install_github("xiaorudong/Escort")The following packages are required for installing Escort. If installation fails, you may need to manually install the dependencies using the function 'install.packages' for CRAN packages or 'BiocManager::install' for Bioconductor packages.
- CRAN packages: alphahull, fastICA, Rtsne, umap, rstatix, DT, FNN, grDevices, Hmisc, jmuOutlier, shotGroups, parallelDist, robustbase, scales, SCORPIUS, sfsmisc, ash shiny, shinycssloaders, shinydashboard, shinyjs, shinyWidgets, dplyr, DelayedMatrixStats
- Bioconductor packages: SingleCellExperiment, SC3, slingshot, clusterProfiler, org.Hs.eg.db, org.Mm.eg.db, edgeR, limma
For any other installation issues/questions please leave a message on our Github Issues.
After successful installation, Escort and related packages need be loaded into the working space:
library(Escort)To use Escort as a Shiny App locally:
library(shiny)
library(shinydashboard)
Escort::shinyEscort()Many more details and examples on how to use the Shiny App or functions directly in R are located in the vignettes available at the website:
-
Xiaoru Dong, PhD (xdong1@ufl.edu)
Department of Biostatistics, University of Florida -
Rhonda Bacher, PhD (rbacher@ufl.edu)
Department of Biostatistics, University of Florida