R Data Package for Long et al. v1.0.0

This is an R data package containing the source data for the scRNA-seq analysis in the Long et al. paper.  This package contains only data and is meant to be used together with the analysis code available at https://github.com/blaserlab/baiocchi_long.

Steps to Reproduce Selected Figures

1.  System Requirements

• R v4.2 or greater
• Rstudio
• This software has been tested on Linux Ubuntu 18.04.6 and Windows 10
• Loading the complete dataset occupies approximately 4 GB memory.

2.  Installation

• download this data set in a convenient location on your system. This contains the processed data required for this analysis project to function.
• clone the analysis project to your computer using git clone https://github.com/blaserlab/baiocchi_long.git
• open the R project by double-clicking on the baiocchi_long.Rproj file
• a list of the packages required for the project can be found in library_catalogs/blas02_baiocchi_lnog.tsv. Filter for packages with status == "active". Install these packages.
• install custom packages from our R Universe repository using these commands:
• install.packages('blaseRtools', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))
• install.packages('blaseRtemplates', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))
• install.packages('blaseRdata', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))
• source R/dependencies.R (the final line in that file must be edited to point to the directory containing the data package)
• source R/configs.R (the file paths defining the figs_out and tables_out variables should be customized for your system)
• typical time required for the first installation and data loading is approximately 15 minutes. This excludes the time required to download the data package.

3.  Instructions for use after installing and configuring

• source R/dependencies.R
• source R/configs.R
• run the code on manuscript_figs.R to generate the desired figure
• each data object used to generate a figure has it's own help manual
• type ?data_object_name to get the help manual
• to review the processing code used to generate that data object, go to the installed location of baiocchi.long.datapkg on your system, enter the data-raw directory and run grep --include=*.R -rnw '.' -e "data_object_name"