Package Recipe 'bioconductor-nestlink'

recipe bioconductor-nestlink

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

Homepage:: https://bioconductor.org/packages/3.20/data/experiment/html/NestLink.html
License:: GPL
Recipe:: /bioconductor-nestlink/meta.yaml

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.

package bioconductor-nestlink¶

Versions:

1.26.0-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.10.0-1, 1.10.0-0, 1.8.0-0, 1.6.0-1,

1.26.0-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.10.0-1, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.6.0-0, 1.4.0-0, 1.2.0-0, 1.0.0-1

Depends:

on bioconductor-annotationhub >=4.0.0,<4.1.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-data-packages >=20260207
on bioconductor-experimenthub >=3.0.0,<3.1.0
on bioconductor-shortread >=1.68.0,<1.69.0
on curl
on r-base >=4.5,<4.6.0a0
on r-gplots >=3.0
on r-protviz >=0.4

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-nestlink

to add into an existing workspace instead, run:

pixi add bioconductor-nestlink

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-nestlink

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-nestlink

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-nestlink:<tag>

(see bioconductor-nestlink/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-nestlink/README.html)