- recipe bioconductor-msnid
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
- Homepage:
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: msnid, doi: 10.1038/nmeth.3252
Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.
- package bioconductor-msnid¶
- versions:
1.36.0-0,1.34.0-0,1.32.0-1,1.32.0-0,1.28.0-2,1.28.0-1,1.28.0-0,1.26.0-0,1.24.0-1,1.36.0-0,1.34.0-0,1.32.0-1,1.32.0-0,1.28.0-2,1.28.0-1,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.22.0-0,1.20.0-0,1.18.1-0,1.16.1-0,1.12.1-0- depends bioconductor-annotationdbi:
>=1.64.0,<1.65.0- depends bioconductor-annotationdbi:
>=1.64.1,<1.65.0a0- depends bioconductor-annotationhub:
>=3.10.0,<3.11.0- depends bioconductor-annotationhub:
>=3.10.0,<3.11.0a0- depends bioconductor-biobase:
>=2.62.0,<2.63.0- depends bioconductor-biobase:
>=2.62.0,<2.63.0a0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocstyle:
>=2.30.0,<2.31.0- depends bioconductor-biocstyle:
>=2.30.0,<2.31.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-msmstests:
>=1.40.0,<1.41.0- depends bioconductor-msmstests:
>=1.40.0,<1.41.0a0- depends bioconductor-msnbase:
>=2.28.0,<2.29.0- depends bioconductor-msnbase:
>=2.28.1,<2.29.0a0- depends bioconductor-mzid:
>=1.40.0,<1.41.0- depends bioconductor-mzid:
>=1.40.0,<1.41.0a0- depends bioconductor-mzr:
>=2.36.0,<2.37.0- depends bioconductor-mzr:
>=2.36.0,<2.37.0a0- depends bioconductor-protgenerics:
>=1.34.0,<1.35.0- depends bioconductor-protgenerics:
>=1.34.0,<1.35.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx-ng:
>=12- depends r-base:
>=4.3,<4.4.0a0- depends r-data.table:
- depends r-doparallel:
- depends r-dplyr:
- depends r-foreach:
- depends r-ggplot2:
- depends r-iterators:
- depends r-purrr:
- depends r-r.cache:
- depends r-rcpp:
- depends r-reshape2:
- depends r-rlang:
- depends r-runit:
- depends r-stringr:
- depends r-tibble:
- depends r-xtable:
- 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-msnid and update with:: mamba update bioconductor-msnid
To create a new environment, run:
mamba create --name myenvname bioconductor-msnid
with
myenvnamebeing 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-msnid:<tag> (see `bioconductor-msnid/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-msnid/README.html)
