hermes
Bioc currentPreprocessing, analyzing, and reporting of RNA-seq data
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
77 64 exported
Complexity
2.2 avg / 7 max
Call network
77 nodes / 69 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
12,310
Files
162
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
80
Internal functions
8
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
2.32
testthat edition
3
Docs
Roxygen coverage
97.5%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
19.4%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
Apache License 2.0
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-05-05
Latest release
2026-04-28
Avg cadence
178 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 77 (1 internal)includes a package overview page
- Examples that run
- 100%69 run in a plain check (6 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 98%
- Help pages citing references
- 3% with a bibliography file
Repository practices
17 development-tooling and community-health practices detected across 8 families in the upstream repository
Checks run against github.com/insightsengineering/hermes on 2026-10-25.
Funding links: pharmaverse.org
GitHub Pages site last deployed 2025-09-03
pkgdown site last built 2025-05-26
Show all practicesHide 4 practices
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| expression_set | – | – | – |
| hermes_data | – | – | – |
| multi_assay_experiment | – | – | – |
| summarized_experiment | – | – | – |
Topics
People
- Daniel Sabanés Bové author maintainer
- Carolyn Zhang author
- F. Hoffmann-La Roche AG copyright holder funder
- Namrata Bhatia author
- Stefanie Bienert author
- Naomi Chang author
- Benoit Falquet author
- Haocheng Li author
- Chendi Liao author
- Jeff Luong author
- Lyndsee Midori Zhang author
- Joseph N. Paulson author
- Alex Richardson author
- Simona Rossomanno author
- Tim Treis author
- Mark Yan author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("hermes")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.