DOI: 10.18129/B9.bioc.NestLink    

This is the development version of NestLink; to use it, please install the devel version of Bioconductor.

NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles

Bioconductor version: Development (3.10)

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.

Author: Pascal Egloff [aut] , Iwan Zimmermann [ctb] , Fabian M. Arnold [ctb], Cedric A.J. Hutter [ctb] , Lennart Opitz [aut] , Lucy Poveda [ctb] , Hans-Anton Keserue [ctb], Christian Panse [aut, cre] , Bernd Roschitzki [aut] , Markus Seeger [aut]

Maintainer: Christian Panse <cp at>

Citation (from within R, enter citation("NestLink")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script 0. Simulate flycode properties.
HTML R Script 1. Link high quality flycode and nanobody sequences by NGS filtering.
HTML R Script 2. Analyze flycode detectability using ESP and SSRC prediction
HTML R Script 3. Compare Predicted and Observed flycodes hydrophobicity values using F255744.
HTML R Script 4. Control experiment to assess the robustness of protein detection via flycodes (NMETH-A35040 Suppl. notes 1).
HTML R Script 5. make-data
PDF   Reference Manual
Text   NEWS


biocViews ExperimentData, ExperimentHub, MassSpectrometryData, ReproducibleResearch, SequencingData
Version 1.1.0
License GPL
Depends R (>= 3.6), AnnotationHub(>= 2.15.3), ExperimentHub(>= 0.99.6), Biostrings(>= 2.51.1), gplots (>= 3.0.0), protViz (>= 0.4.0), ShortRead(>= 1.41.0)
Imports grDevices, graphics, stats, utils
Suggests BiocStyle(>= 2.2.0), DT, ggplot2, knitr, rmarkdown, testthat, specL, lattice, scales
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package NestLink_1.1.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: