R 4.4.3 is needed

Reference: https://compgenomr.github.io/book/software-information-and-conventions.html#packages-needed-to-run-the-book-code

1. Core Bioconductor and dependencies packages

install.packages("BiocManager")
# install bioconductor package "rtracklayer"
BiocManager::install("rtracklayer")

install.packages(c("tidyverse", "snpStats", "knitr", "tidyr", "data.table" ))

# dependencies
install.packages(c("Matrix", "dotCall64", "spam", "spatstat.random", "deldir", 
                   "SeuratObject", "RSpectra", "spatstat.explore", 
                   "spatstat.geom", "uwot", "RcppEigen"))

2. Packages for Genomic Data Analysis

You can also embed plots, for example:

# For working with genomic ranges and sequences
BiocManager::install(c("GenomicRanges", "Biostrings", "BSgenome"))

# For working with and annotating genomes
BiocManager::install(c("AnnotationDbi", "org.Hs.eg.db", "TxDb.Hsapiens.UCSC.hg38.knownGene", "TxDb.Hsapiens.UCSC.hg19.knownGene"))

# For analyzing high-throughput sequencing data
BiocManager::install(c("Rsamtools", "Rsubread", "GenomicAlignments", "ShortRead"))

# For handling single-cell data
BiocManager::install(c("SingleCellExperiment", "scran", "scater", "Seurat", "loomR"))

3. Packages for RNA-Seq Analysis

# For differential expression analysis
BiocManager::install(c("DESeq2", "edgeR", "limma"))

# For transcript assembly and quantification
BiocManager::install("ballgown")

# For visualization of RNA-Seq data
BiocManager::install(c("pheatmap", "EnhancedVolcano"))

4. Epigenetics and Methylation Analysis

# Variant annotation and visualization
BiocManager::install(c("VariantAnnotation", "SNPRelate", "vcfR"))

# Tools for structural variation
BiocManager::install("StructuralVariantAnnotation")

5. Variant Analysis

# Variant annotation and visualization
BiocManager::install(c("VariantAnnotation", "SNPRelate"))

# Tools for structural variation
BiocManager::install("StructuralVariantAnnotation")

6. Functional Annotation

# General plotting tools
install.packages(c("cowplot", "ggpubr"))

8. Single-Cell Analysis

# Analysis and visualization
BiocManager::install(c("SingleR", "scRNAseq"))

Seurat and loomR

# Workflow and pipeline tools
BiocManager::install("BiocParallel")
BiocManager::install(SeuratObject")

remotes::install_version(package = 'Seurat', version = package_version('5.1.0'))

# Install devtools from CRAN
install.packages("devtools")

# Use devtools to install hdf5r and loomR from GitHub
devtools::install_github("hadley/stringr")
devtools::install_github(repo = "hhoeflin/hdf5r")
devtools::install_github(repo = "mojaveazure/loomR", ref = "develop")

9. Machine Learning and Data Processing

# Machine learning frameworks
install.packages(c("caret", "randomForest"))

10. Other Utilities

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c('qvalue','plot3D',
                      'cluster', 'NbClust', 'fastICA', 'NMF','matrixStats',
                      'Rtsne', 'mosaic', 'genomation',
                      'ggbio', 'Gviz',  'RUVSeq',
                      'gProfileR', 'ggfortify', 'corrplot',
                      'gage', 'EDASeq', 'citr', 'formatR',
                      'svglite', 'Rqc', 'ShortRead', 'QuasR',
                      'methylKit','FactoMineR', 'iClusterPlus',
                      'enrichR','xgboost','glmnet',
                      'DALEX','kernlab','pROC','nnet','RANN',
                      'ranger','GenomeInfoDb', 
                      'ComplexHeatmap', 'circlize', 
                      'rtracklayer', 'BSgenome.Hsapiens.UCSC.hg38',
                      'BSgenome.Hsapiens.UCSC.hg19',
                      'AnnotationHub', 'GenomicFeatures', 'normr',
                      'MotifDb', 'TFBSTools', 'rGADEM', 'JASPAR2018'
                     ))
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes") }
remotes::install_github("mojaveazure/seurat-disk")

ChIP Seq

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("clusterProfiler", force = TRUE)
BiocManager::install("ChIPseeker")
BiocManager::install("EnsDb.Hsapiens.v75")