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Bioconductor Packages: Development, Maintenance, and Peer Review
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Table of contents
Welcome
Package Submissions
Overview
1
Bioconductor Package Submissions
Package Development Guidelines
Overview
2
Package name
3
General Bioconductor Package Development
4
Important Bioconductor Package Development Features
5
Common Bioconductor Methods and Classes
6
The README file
7
The DESCRIPTION file
8
The NAMESPACE file
9
The NEWS file
10
The LICENSE file
11
The CITATION file
12
The INSTALL file
13
Documentation
14
Package data
15
Unit tests
16
R code
17
Fortran / C / C++ / Python / Third-Party Code
18
Shiny apps
19
AI policy and Third Party Code
20
Non-Software Packages
21
The .gitignore file
22
Build / Check / BiocCheck
23
Conclusion
Bioconductor Package Maintenance
Overview
24
Git Version Control
25
Version Numbering
26
Troubleshooting Build Report
27
Debugging C/C++ code
28
Deprecation Guidelines
29
Package End of Life Policy
30
Branch Rename FAQs
Package Reviewer Resources
Overview
31
Review Expectations
32
Reviewer Resources and Tools
33
Volunteer to Review
Appendix
A
Using the ‘Devel’ Version of Bioconductor
B
Advanced Build Options
C
Querying Web Resources
D
C and Fortran code
E
C++/Mavericks Best Practices
F
Debug: Links in Rd files
G
NEWS
H
References
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H
References
Soneson, Charlotte, Lori Shepherd, Marcel Ramos, et al. 2025.
“Eleven Quick Tips for Writing a Bioconductor Package.”
PLoS Comput. Biol.
21 (3): e1012856.
https://doi.org/10.1371/journal.pcbi.1012856
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G
NEWS
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H
References
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