recipe bioconductor-topdownr

Investigation of Fragmentation Conditions in Top-Down Proteomics

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/topdownr.html

License:

GPL (>= 3)

Recipe:

/bioconductor-topdownr/meta.yaml

The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

package bioconductor-topdownr

Versions:

1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.1-0

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-msnbase >=2.24.0,<2.25.0

• bioconductor-mzr >=2.32.0,<2.33.0

• bioconductor-protgenerics >=1.30.0,<1.31.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-base >=4.2,<4.3.0a0

• r-ggplot2 >=2.2.1

• r-matrix >=1.4-2

Required By:

• bioconductor-topdownrdata

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-topdownr

and update with:

conda update bioconductor-topdownr

or use the docker container:

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

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

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Link to this page

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