recipe bioconductor-dialignr

Dynamic Programming Based Alignment of MS2 Chromatograms

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/DIAlignR.html

License:

GPL-3

Recipe:

/bioconductor-dialignr/meta.yaml

Links:

usegalaxy-eu: dialignr

To obtain unbiased proteome coverage from a biological sample, mass-spectrometer is operated in Data Independent Acquisition (DIA) mode. Alignment of these DIA runs establishes consistency and less missing values in complete data-matrix. This package implements dynamic programming with affine gap penalty based approach for pair-wise alignment of analytes. A hybrid approach of global alignment (through MS2 features) and local alignment (with MS2 chromatograms) is implemented in this tool.

package bioconductor-dialignr

versions:

2.10.0-0,  2.8.0-0,  2.6.0-1,  2.6.0-0,  2.2.0-2,  2.2.0-1,  2.2.0-0,  2.0.0-0,  1.2.0-1, 

2.10.0-0,  2.8.0-0,  2.6.0-1,  2.6.0-0,  2.2.0-2,  2.2.0-1,  2.2.0-0,  2.0.0-0,  1.2.0-1,  1.2.0-0,  1.0.5-0

depends bioconductor-mzr:

>=2.36.0,<2.37.0

depends bioconductor-mzr:

>=2.36.0,<2.37.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-bit64:

depends r-data.table:

depends r-dbi:

depends r-dplyr:

depends r-ggplot2:

depends r-magrittr:

depends r-phangorn:

depends r-pracma:

depends r-rcpp:

depends r-rcppeigen:

depends r-reticulate:

depends r-rlang:

depends r-rmsnumpress:

depends r-rsqlite:

depends r-signal:

depends r-tidyr:

depends r-zoo:

>=1.8-3

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-dialignr

and update with::

   mamba update bioconductor-dialignr

To create a new environment, run:

mamba create --name myenvname bioconductor-dialignr

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-dialignr/tags`_ for valid values for ``<tag>``)

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