NestLink
Bioc currentNestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Provides next-generation sequencing (NGS) and mass spectrometry (MS) sample data, code snippets and replication material used for developing NestLink. The NestLink approach is a protein binder selection and identification technology able to biophysically characterize thousands of library members at once without handling individual clones at any stage of the process. Data were acquired on NGS and MS platforms at the Functional Genomics Center Zurich.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
33 14 exported
Complexity
2.1 avg / 11 max
Call network
33 nodes / 16 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
4,063
Files
51
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
17
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.08
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
60%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6
System requirements
–
C++ standard
–
License
GPL
License flags
not SPDX, not OSI
History
Versions
15
First release
2019-05-02
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 17
- Examples that run
- 100%17 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 87%
- Return-value docs
- 100%
- Help pages citing references
- 6%
- 2. Analyze flycode detectability using ESP and SSRC prediction HTML
- 3. Compare Predicted and Observed flycodes hydrophobicity values using F255744. HTML
- 1. Link high quality flycode and nanobody sequences by NGS filtering. HTML
- 5. make-data HTML
- 0. Simulate flycode properties. HTML
- 4. Control experiment to assess the robustness of protein detection via flycodes (NMETH-A35040 Suppl. notes 1). HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| metadata | data.frame | 8 × 17 | No other package |
Topics
People
- Lennart Opitz author maintainer
- Fabian M. Arnold contributor
- Pascal Egloff author
- Cedric A.J. Hutter contributor
- Hans-Anton Keserue contributor
- Christian Panse author contributor
- Lucy Poveda contributor
- Bernd Roschitzki author
- Markus Seeger author
- Iwan Zimmermann contributor
- Damien Morger
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("NestLink")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.