3A - Initialize R environment

Load Conda derived R environment.

.libPaths('/project/.conda/envs/r-4.4.1-env/lib/R/library')
options(stringsAsFactors = FALSE)

packages <- c(
  # Core data / plotting
  "svglite", "fastSave", "data.table", "dplyr", "ggplot2", "reshape2", "patchwork",
  "ggstatsplot", "ggpubr", "ggalluvial", "tibble",
  "scCustomize", "ggplotify", "gridExtra", "ggforce",

  # Genomics annotation
  "EnsDb.Mmusculus.v79", "BSgenome.Mmusculus.UCSC.mm39", "AnnotationHub",

  # Single-cell analysis
  "Seurat", "SeuratData", "SeuratDisk", "SeuratWrappers", "Seurat.utils",
  "Signac", "sctransform", "glmGamPoi", "harmony", "ComplexHeatmap", "Matrix",

  # Epigenomics
  "chromVAR", "JASPAR2024", "TFBSTools", "motifmatchr", "MotifDb",

  # Trajectory and GRN
  "monocle3", "cicero", "Pando", "xgboost", "universalmotif",

  # Pathway scoring and gene sets
  "UCell", "SCPA", "GSEABase", "SiPSiC", "msigdbr",

  # Parallelization
  "BiocParallel", "parallelly",

  # Differential expression / statistics
  "pROC"
)

invisible(lapply(packages, function(x) {
  suppressMessages(suppressPackageStartupMessages(library(x, character.only = TRUE)))
}))

source("extra_functions.R")

set.seed(99)

SMMHC^CreERT2;R26R^tdTomato;Ren1^cYFP mice

Set file paths to Cellranger ARC outputs.

sample_name <- "captopril-multiome"
processed_dir <- "/processed/cellranger_analysis/"

file_paths <- data.table(sample = c("captopril-ctrl_1mo", "captopril-ctrl_3mo",
                                    "captopril-ctrl_6mo", "captopril-trt_1mo",
                                    "captopril-trt_3mo", "captopril-trt_6mo"),
    counts_path = c(file.path(processed_dir, "captopril-ctrl_1mo/outs/filtered_feature_bc_matrix.h5"),
                    file.path(processed_dir, "captopril-ctrl_3mo/outs/filtered_feature_bc_matrix.h5"),
                    file.path(processed_dir, "captopril-ctrl_6mo_manual/outs/filtered_feature_bc_matrix.h5"),
                    file.path(processed_dir, "captopril-trt_1mo/outs/filtered_feature_bc_matrix.h5"),
                    file.path(processed_dir, "captopril-trt_3mo/outs/filtered_feature_bc_matrix.h5"),
                    file.path(processed_dir, "captopril-trt_6mo/outs/filtered_feature_bc_matrix.h5")),
    frag_path = c(file.path(processed_dir, "captopril-ctrl_1mo/outs/atac_fragments.tsv.gz"),
                    file.path(processed_dir, "captopril-ctrl_3mo/outs/atac_fragments.tsv.gz"),
                    file.path(processed_dir, "captopril-ctrl_6mo_manual/outs/atac_fragments.tsv.gz"),
                    file.path(processed_dir, "captopril-trt_1mo/outs/atac_fragments.tsv.gz"),
                    file.path(processed_dir, "captopril-trt_3mo/outs/atac_fragments.tsv.gz"),
                    file.path(processed_dir, "captopril-trt_6mo/outs/atac_fragments.tsv.gz")))