Data used in SeuratIntegrate paper

This repository stores the data used to generate hepatocellular carcinoma analyses in the paper presenting SeuratIntegrate. It contains the scripts to reproduce the figure 1 presented in the article.To be able to fully reproduce the results from the paper, one shoud:

download all the files

install R 4.3.3, with correspondig base R packages (stats, graphics, grDevices, utils, datasets, methods and base)

install R packages listed in the file sessionInfo.out

install the provided version of SeuratIntegrate. In an R session, run:

remotes::install_local("path/to/SeuratIntegrate_0.4.0.tar.gz")

install (mini)conda (we used version 23.11.0) if not already

install conda environments:

conda create -n SeuratIntegrate_bbknn –file SeuratIntegrate_bbknn_package-list.txt
conda create -n SeuratIntegrate_scanorama –file SeuratIntegrate_scanorama_package-list.txt

make them usable by SeuratIntegrate by opening an R session and:

library(SeuratIntegrate)

UpdateEnvCache("bbknn", conda.env = "SeuratIntegrate_bbknn", conda.env.is.path = FALSE)
UpdateEnvCache("scanorama", conda.env = "SeuratIntegrate_scanorama", conda.env.is.path = FALSE)

Once done, the file integrate.R should produce reproducible results. Note that lines 3 to 6 from integrate.R should be adapted to the user's setup.