To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("MSnID")
In most cases, you don't need to download the package archive at all.
MSnID
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications.
Bioconductor version: 3.0
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.
Author: Vlad Petyuk with contributions from Laurent Gatto
Maintainer: Vlad Petyuk <petyuk at gmail.com>
Citation (from within R,
enter citation("MSnID")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("MSnID")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MSnID")
| R Script | MSnID Package for Handling MS/MS Identifications | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | MassSpectrometry, Proteomics, Software |
| Version | 1.0.1 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), Rcpp |
| Imports | MSnbase(>= 1.12.1), mzID(>= 1.3.5), R.cache, foreach, doParallel, parallel, reshape2, methods, iterators, data.table, Biobase, mzR |
| LinkingTo | |
| Suggests | BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | RforProteomics |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | MSnID_1.0.1.tar.gz |
| Windows Binary | MSnID_1.0.1.zip |
| Mac OS X 10.6 (Snow Leopard) | MSnID_1.0.1.tgz |
| Mac OS X 10.9 (Mavericks) | MSnID_1.0.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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