How insightsengineering/hermes works
hermes is an R package for preprocessing, analyzing, and reporting RNA-seq data. Its documented capabilities span importing counts into a ready-to-analyze format, gene annotation, QC, filtering, normalization, visualization, PCA, differential expression, and templated QC reporting. The graph groups these stages around the HermesData representation and analysis tools. No source excerpts were provided, so implementation links and call ownership cannot be verified; dashed edges indicate documented capabilities or integrations, not confirmed runtime sequencing.
Main entry points: HermesData-class.R HermesData model · data.R Count import · connections.R Gene annotation · quality.R QC flags
Components 12
Data and annotation
- Count import
R/data.R - HermesData model
R/HermesData-class.R - Gene annotation
R/connections.R
Preprocessing and QC
- QC flags
R/quality.R - Data filtering
R/HermesData-methods.R - Normalization
R/normalization.R
Analysis and reporting
- Descriptive plots
R/draw_barplot.R - PCA
R/pca.R - Differential expression
R/differential.R - QC report template
inst/rmarkdown/templates/qc_report/template.yaml
Other components
- Analyst
- BioMart
Connections 11
- Analyst → Count import: imports counts
README.md - Count import → HermesData model: creates ready format
README.md - HermesData model → Gene annotation: annotates genes
README.md - Gene annotation → BioMart: queries annotation
README.md - HermesData model → QC flags: adds QC flags
README.md - HermesData model → Data filtering: filters dataset
README.md - HermesData model → Normalization: normalizes counts
README.md - HermesData model → Descriptive plots: produces plots
README.md - HermesData model → PCA: performs PCA
README.md - HermesData model → Differential expression: analyzes expression
README.md - QC flags → QC report template: reports QC
README.md