NestLink

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 (3.9)

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

Maintainer: Christian Panse <cp at fgcz.ethz.ch>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("NestLink", version = "3.9")

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")

 

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 NestLink data for ExperimentHub.
PDF   Reference Manual
Text   NEWS

Details

biocViews ExperimentData, ExperimentHub, MassSpectrometryData, ReproducibleResearch, SequencingData
Version 0.99.95
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
LinkingTo
Suggests BiocStyle(>= 2.2.0), DT, ggplot2, knitr, rmarkdown, testthat, specL, lattice, scales
SystemRequirements
Enhances
URL
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_0.99.95.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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 http://bioconductor.org/packages/NestLink/
Package Downloads Report Download Stats

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