cpanse/nestlink repository overview

⁠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

⁠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