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R Package Requirements for Gene Downloader Scripts

CRAN Packages (install via install.packages())

  • dplyr # Data manipulation and transformation
  • readr # Reading and writing data files
  • tools # R development tools
  • httr # HTTP requests for API calls
  • httr2 # Modern HTTP requests (alternative to httr)
  • jsonlite # JSON data parsing
  • rvest # Web scraping
  • xml2 # XML parsing
  • stringr # String manipulation
  • tidyr # Data tidying and reshaping
  • purrr # Functional programming tools
  • curl # HTTP requests (alternative backend)
  • RCurl # Alternative HTTP client
  • data.table # Fast data manipulation
  • magrittr # Pipe operators
  • tibble # Modern data frames
  • vroom # Fast file reading
  • rentrez # NCBI E-utilities access
  • easyPubMed # PubMed data extraction
  • europepmc # Europe PMC API access
  • geneLenDataBase # Gene length information
  • GenomicRanges # Genomic ranges manipulation

Bioconductor Packages (install via BiocManager::install())

  • gwasrapidd # GWAS Catalog API access
  • biomaRt # Biomart database access
  • GO.db # Gene Ontology database
  • org.Hs.eg.db # Human gene annotations
  • AnnotationDbi # Annotation database interface
  • KEGGREST # KEGG pathway REST API
  • ReactomePA # Reactome pathway analysis
  • reactome.db # Reactome database
  • GenomicFeatures # Genomic features extraction
  • TxDb.Hsapiens.UCSC.hg38.knownGene # Human genome annotations
  • BSgenome.Hsapiens.UCSC.hg38 # Human genome sequence
  • VariantAnnotation # Variant annotation tools
  • gwascat # GWAS catalog data access
  • SNPlocs.Hsapiens.dbSNP144.GRCh38 # SNP locations
  • MafDb.1Kgenomes.phase3.hs37d5 # Minor allele frequencies
  • PolyPhen.Hsapiens.dbSNP131 # PolyPhen predictions
  • SIFT.Hsapiens.dbSNP137 # SIFT predictions
  • LDlinkR # LD Link API access
  • haploR # HaploReg API access
  • rsnps # SNP database access
  • myvariant # MyVariant.info API access

Installation Commands

Install all packages automatically:

# Run the requirements script
Rscript requirements.R install

Manual installation:

# Install CRAN packages
cran_packages <- c("dplyr", "readr", "tools", "httr", "httr2", "jsonlite", "rvest", "xml2", "stringr", 
                   "tidyr", "purrr", "curl", "RCurl", "data.table", "magrittr", "tibble", "vroom",
                   "rentrez", "easyPubMed", "europepmc", "geneLenDataBase", "GenomicRanges")
install.packages(cran_packages)

# Install Bioconductor packages
if (!require(BiocManager, quietly = TRUE)) install.packages("BiocManager")
bioc_packages <- c("gwasrapidd", "biomaRt", "GO.db", "org.Hs.eg.db", "AnnotationDbi", "KEGGREST", 
                   "ReactomePA", "reactome.db", "GenomicFeatures", "TxDb.Hsapiens.UCSC.hg38.knownGene",
                   "BSgenome.Hsapiens.UCSC.hg38", "VariantAnnotation", "gwascat", 
                   "SNPlocs.Hsapiens.dbSNP144.GRCh38", "MafDb.1Kgenomes.phase3.hs37d5",
                   "PolyPhen.Hsapiens.dbSNP131", "SIFT.Hsapiens.dbSNP137", "LDlinkR", 
                   "haploR", "rsnps", "myvariant")
BiocManager::install(bioc_packages)

Package Usage by Script

download_gene2.R (main script)

  • dplyr, readr, tools, httr, jsonlite

gwasrapidd.R

  • gwasrapidd, dplyr

gwas_rest_api.R

  • httr, jsonlite

opentargets.R

  • httr, jsonlite

disgenet.R

  • httr, rvest, xml2

pubmed.R

  • httr, jsonlite

biomart.R

  • biomaRt, dplyr, stringr

gene_ontology.R

  • GO.db, org.Hs.eg.db, AnnotationDbi, dplyr, stringr

kegg_pathways.R

  • KEGGREST, org.Hs.eg.db, AnnotationDbi, dplyr, stringr

reactome_pathways.R

  • ReactomePA, reactome.db, org.Hs.eg.db, AnnotationDbi, dplyr, stringr

curated_genes.R

  • No additional packages (uses base R)