README.md

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

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:

1. Derive Peptide FlyCodes by Conducting Random Experiment
2. NGS filtering workflow to get high quality FlyCode and Nanobody sequences
3. FASTA p1875 db10 - ESP / SSRC prediction - Summary
4. Compare Predicted and Measured FlyCodes (F255744).
5. 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')

References

• project p1875 at the Functional Genomics Center Zurich

• bioRxiv 2018/03/23/287813

• DOI:10.1038/s41592-019-0389-8

cpanse/NestLink documentation built on May 16, 2022, 2:33 a.m.