NestLink

Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles

available for download in the ‘Devel’ version of Bioconductor using BiocManager::install("NestLink").
The package ‘landing page’ is available at https://bioconductor.org/packages/NestLink
(since 2019-01-14)

1. System requirements

Software dependencies

install R (>= 3.6)
install Bioconductor (>=3.9)

2. Installation guide

run an R session and execute the following R code snippet

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

or using docker

docker pull cpanse/nestlink \
  && docker run -a stdin -a stdout -i -t cpanse/nestlink /scratch/R-devel/bin/R

Typical install time -
based on the Dockerfile the install snippet above
took 19m46.464s on a linux server (RAID6, Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz) and one hour on dockerhub.

As an alternative you can also consider the latest release.

Versions the software has been tested on

platform	NestLink version	platform version	R version	note
Linux	0.99.51	Debian 10 (buster)	R 3.5.1, Bioconductor version 3.8	CP
Microsoft	0.99.51	Server 2012 R2 x64	R 3.5.0, Bioconductor version 3.7
macOS High	0.99.51	Sierra 10.13.4	R 3.4.2

3. Demonstration / Documentation

Instructions to run on data and expected output is described in the package’s
vignettes.

browseVignettes('NestLink')

please study the vignettes in the following order:

Derive Peptide FlyCodes by Conducting Random Experiment
NGS filtering workflow to get high quality FlyCode and Nanobody sequences
FASTA p1875 db10 - ESP / SSRC prediction - Summary
Compare Predicted and Measured FlyCodes (F255744).
Control experiment to assess robustness of protein detection via flycodes

Expected run time for the vignette build is less than 5 minutes on a today’s desktop computer.

4. Instructions for use

read the vignettes.

browseVignettes('NestLink')