Package Recipe 'bioconductor-customprodb'

recipe bioconductor-customprodb

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/customProDB.html
License:: Artistic-2.0
Recipe:: /bioconductor-customprodb/meta.yaml

Database search is the most widely used approach for peptide and protein identification in mass spectrometry-based proteomics studies. Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification. More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific. Here, we report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search. This work bridges genomics and proteomics studies and facilitates cross-omics data integration.

package bioconductor-customprodb¶

Versions:

1.46.0-0, 1.41.0-0, 1.40.0-0, 1.38.0-0, 1.34.0-0, 1.32.0-0, 1.30.0-1, 1.30.0-0, 1.28.0-0,

1.46.0-0, 1.41.0-0, 1.40.0-0, 1.38.0-0, 1.34.0-0, 1.32.0-0, 1.30.0-1, 1.30.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.22.0-0, 1.14.0-0

Depends:

on bioconductor-annotationdbi >=1.68.0,<1.69.0
on bioconductor-biomart >=2.62.0,<2.63.0
on bioconductor-biostrings >=2.74.0,<2.75.0
on bioconductor-genomeinfodb >=1.42.0,<1.43.0
on bioconductor-genomicalignments >=1.42.0,<1.43.0
on bioconductor-genomicfeatures >=1.58.0,<1.59.0
on bioconductor-genomicranges >=1.58.0,<1.59.0
on bioconductor-iranges >=2.40.0,<2.41.0
on bioconductor-rsamtools >=2.22.0,<2.23.0
on bioconductor-rtracklayer >=1.66.0,<1.67.0
on bioconductor-s4vectors >=0.44.0,<0.45.0
on bioconductor-txdbmaker >=1.2.0,<1.3.0
on bioconductor-variantannotation >=1.52.0,<1.53.0
on r-ahocorasicktrie
on r-base >=4.4,<4.5.0a0
on r-dbi
on r-plyr
on r-rcurl
on r-rsqlite
on r-stringr

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-customprodb

to add into an existing workspace instead, run:

pixi add bioconductor-customprodb

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-customprodb

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-customprodb

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-customprodb:<tag>

(see bioconductor-customprodb/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-customprodb/README.html)