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source("http://bioconductor.org/biocLite.R")
biocLite("MSstats")
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MSstats
Protein Significance Analysis in LC-MS, SRM and DIA for Label-free or Label-based Proteomics Experiments
Bioconductor version: 2.13
A set of tools for protein significance analysis in label-free or LC-MS, SRM and DIA experiments.
Author: Meena Choi <choi67 at purdue.edu>, Ching-Yun Chang <chang54 at purdue.edu>, Olga Vitek <ovitek at purdue.edu>
Maintainer: Meena Choi <choi67 at purdue.edu>
Citation (from within R,
enter citation("MSstats")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("MSstats")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MSstats")
| Comparison1.pdf | ||
| Comparison2.pdf | ||
| Condition1.pdf | ||
| Condition2.pdf | ||
| DIA_constant_QQPlot4.pdf | ||
| DIA_constant_ResidualPlot4.pdf | ||
| DIA_ProfilePlot_269.pdf | ||
| DIA_ProfilePlot_377.pdf | ||
| Heatmap45Yeast1.pdf | ||
| Heatmap45Yeast2.pdf | ||
| LCMS_constant_ResidualPlot.pdf | ||
| LCMS_Heatmap.pdf | ||
| LCMS_ProfilePlot.pdf | ||
| MSstatsOverview.pdf | ||
| power.pdf | ||
| ProfilePlot1.pdf | ||
| ProfilePlot2.pdf | ||
| R Script | Protein quantification in LC-MS, SRM, DIA experiments | |
| QCPlot_all.pdf | ||
| QCPlot_all_before.pdf | ||
| QQPlot2.pdf | ||
| ResidualPlot2.pdf | ||
| SampleSizeReplicateYeast.pdf | ||
| SRM_QQPlot_perFeature_heavy.pdf | ||
| SRM_QQPlot_perFeature_light.pdf | ||
| Volcano45Yeast1.pdf | ||
| Volcano45Yeast2.pdf | ||
| VolcanoYeast1.pdf | ||
| VolcanoYeast2.pdf | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Software |
| Version | 2.0.1 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0), Rcpp, MSnbase |
| Imports | lme4, marray, limma, gplots, ggplot2 |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | MSstats_2.0.1.tar.gz |
| Windows Binary | MSstats_2.0.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | MSstats_2.0.1.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
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