NestLink

This is the released version of NestLink; for the devel version, see NestLink.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

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

Bioconductor version: Release (3.23)

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] ORCID: 0000-0001-8948-3704 , Iwan Zimmermann [ctb] ORCID: 0000-0003-3476-4749 , Fabian M. Arnold [ctb], Cedric A.J. Hutter [ctb] ORCID: 0000-0002-8920-3343 , Lennart Opitz [aut, cre] ORCID: 0000-0001-7945-6737 , Lucy Poveda [ctb] ORCID: 0000-0002-5291-5582 , Hans-Anton Keserue [ctb], Christian Panse [aut, ctb] ORCID: 0000-0003-1975-3064 , Bernd Roschitzki [aut] ORCID: 0000-0001-5756-9773 , Markus Seeger [aut] ORCID: 0000-0003-1761-8571

Maintainer: Lennart Opitz <lopitz at fgcz.ethz.ch>

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

Pascal Egloff, Lennart Opitz, Christian Panse, Bernd Roschitzki, Markus Seeger. NestLink: NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles. doi:10.18129/B9.bioc.NestLink, R package version 1.28.0, https://bioconductor.org/packages/NestLink.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("NestLink")

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

Documentation

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

browseVignettes("NestLink")

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
1. Link high quality flycode and nanobody sequences by NGS filtering.	HTML	R Script
5. make-data	HTML	R Script
0. Simulate flycode properties.	HTML	R Script
4. Control experiment to assess the robustness of protein detection via flycodes (NMETH-A35040 Suppl. notes 1).	HTML	R Script
Reference Manual	PDF
NEWS	Text

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Details

biocViews	ExperimentData, ExperimentHub, MassSpectrometryData, ReproducibleResearch, SequencingData
Version	1.28.0
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 years)
License	GPL
Depends	R (>= 3.6), AnnotationHub (>= 2.15), ExperimentHub (>= 1.0), Biostrings (>= 2.51), gplots (>= 3.0), protViz (>= 0.4), ShortRead (>= 1.41)
Imports	grDevices, graphics, stats, utils
System Requirements
URL

Suggests	BiocStyle (>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat, specL, lattice, scales
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	NestLink_1.28.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/NestLink
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NestLink
Package Short Url	https://bioconductor.org/packages/NestLink/
Package Downloads Report	Download Stats