NestLink
This package is for version 3.15 of Bioconductor; for the stable, up-to-date 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: 3.15
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, cre] , Lucy Poveda [ctb] , Hans-Anton Keserue [ctb], Christian Panse [aut, ctb] , Bernd Roschitzki [aut] , Markus Seeger [aut]
Maintainer: Lennart Opitz <lopitz at fgcz.ethz.ch>
citation("NestLink")):
Installation
To install this package, start R (version "4.2") 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")| 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 | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, MassSpectrometryData, ReproducibleResearch, SequencingData |
| Version | 1.12.0 |
| 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 |
See More
| Suggests | BiocStyle(>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat, specL, lattice, scales |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | NestLink_1.12.0.tar.gz |
| Windows Binary | |
| macOS Binary (x86_64) | |
| 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 |