fmseadatabase

Metabolite and Pathway Databases for fMSEA Analysis

Installation

# Install from GitHub
remotes::install_github("tidymass/fmseadatabase")

Available Databases

MS1 Databases (Total: ~1.7MB)

• kegg_compound_ms1 - KEGG metabolite MS1 database (712KB)
• hmdb_compound_ms1 - HMDB metabolite MS1 database (1.0MB)

Pathway Databases (Total: ~3.6MB)

• kegg_pathway - KEGG metabolic pathways (608KB)
• reactome_pathway - Reactome metabolic pathways (736KB)
• hmdb_pathway - HMDB metabolic pathways (1.0MB)
• imetpd_pathway - IMet-PD metabolic pathways (1.0MB)
• wiki_pathway - WikiPathways database (240KB)

Total package size: ~5.3MB

Usage

library(fmseadatabase)

# Load databases
data("kegg_compound_ms1")
data("kegg_pathway")

# List all available data
data(package = "fmseadatabase")

# Use in fMSEA analysis
# ...

Data Sources

• KEGG: Kyoto Encyclopedia of Genes and Genomes
• HMDB: Human Metabolome Database
• Reactome: Reactome Pathway Database
• IMetPD: Integrated Metabolomics Pipeline for Drug Discovery
• WikiPathways: Community-curated pathway database