NestLink

This is the development version of NestLink; for the stable release version, see NestLink.

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

Bioconductor version: Development (3.21)

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

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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	HTML	R Script
Reference Manual	PDF
NEWS	Text

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Details

biocViews	ExperimentData, ExperimentHub, MassSpectrometryData, ReproducibleResearch, SequencingData
Version	1.23.0
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
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Build Report	Build Report

Package Archives

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

Source Package	NestLink_1.23.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (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