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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
Non-Software Packages
20
The .gitignore file
21
Conclusion
Bioconductor Package Maintenance
Overview
22
Git Version Control
23
Version Numbering
24
Troubleshooting Build Report
25
Debugging C/C++ code
26
Deprecation Guidelines
27
Package End of Life Policy
28
Branch Rename FAQs
Package Reviewer Resources
Overview
29
Review Expectations
30
Reviewer Resources and Tools
31
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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