Analysis scripts for the EquBAL explorer ShinyCell application hosted on SciLifeLab Serve
This is a public repository containing scripts for the analysis described in the publication:
An Interactive Web Resource for Exploring Equine BAL Cell scRNA-seq Data
Sulyaeva J., Fegraeus K., Riihimäki M., Nordlund J., Raine A. (2025)
The funding for this study was provided by FORMAS.
Sequencing data for this project is available at -----. All data has been analyzed on a high performance cluster (HPC) using R. The resulting analysis datasets are available at ----.
The analysis directories are numbered in the order the steps should be executed. Working directory for each script should be the same as the script's location, to align with relative paths.
To run the other scripts in this repository, you will need to do the following:
Install:
- R 3.6.0 and an integrated environment, e.g. RStudio
- R packages: Seurat v.4.3 (!), DoubletFinder, ShinyCell
- Additional R packages required by ShinyCell: data.table, Matrix, hdf5r, reticulate, ggplot2, gridExtra, glue, readr, RColorBrewer, R.utils, shiny, shinyhelper, DT, magrittr, ggdendro
Download the files from ------ and place them in the following directories:
- raw_data/Dropseq : all files from Dropseq folder (n=20)
- raw_data/HIVE : all files from HIVE folder (n=13)
Exceptions:
01_preprocessing/custom_code contains two functions from DoubletFinder package modified manually due to incompatibility with Seurat v.4. These do not require any actions.