Package: DEqMS 1.31.0
Yafeng Zhu
DEqMS: a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
DEqMS is developped on top of Limma. However, Limma assumes same prior variance for all genes. In proteomics, the accuracy of protein abundance estimates varies by the number of peptides/PSMs quantified in both label-free and labelled data. Proteins quantification by multiple peptides or PSMs are more accurate. DEqMS package is able to estimate different prior variances for proteins quantified by different number of PSMs/peptides, therefore acchieving better accuracy. The package can be applied to analyze both label-free and labelled proteomics data.
Authors:
DEqMS_1.31.0.tar.gz
DEqMS_1.31.0.zip(r-4.7)DEqMS_1.31.0.zip(r-4.6)DEqMS_1.31.0.zip(r-4.5)
DEqMS_1.31.0.tgz(r-4.6-any)DEqMS_1.31.0.tgz(r-4.5-any)
DEqMS_1.31.0.tar.gz(r-4.7-any)DEqMS_1.31.0.tar.gz(r-4.6-any)
DEqMS_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DEqMS/json (API)
NEWS
| # Install 'DEqMS' in R: |
| install.packages('DEqMS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yafeng/deqms/issues
On BioConductor:DEqMS-1.31.0(bioc 3.24)DEqMS-1.30.0(bioc 3.23)
immunooncologyproteomicsmassspectrometrypreprocessingdifferentialexpressionmultiplecomparisonnormalizationbayesianexperimenthubsoftwarelimmaquantitative-proteomic-analysis
Last updated from:fcec1ed7d0. Checks:8 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 127 | ||
| linux-devel-x86_64 | ERROR | 208 | ||
| source / vignettes | OK | 200 | ||
| linux-release-x86_64 | ERROR | 197 | ||
| macos-release-arm64 | ERROR | 114 | ||
| macos-oldrel-arm64 | ERROR | 100 | ||
| windows-devel | ERROR | 107 | ||
| windows-release | ERROR | 97 | ||
| windows-oldrel | ERROR | 101 | ||
| wasm-release | OK | 122 |
Exports:equalMedianNormalizationmedianSummarymedianSweepingmedpolishSummaryoutputResultpeptideProfilePlotResidualplotspectraCounteBayesVarianceBoxplotVarianceScatterplot
Dependencies:clicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclelimmamagrittrmatrixStatspillarpkgconfigR6RColorBrewerrlangS7scalesstatmodtibbletidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| normalize to have equal medians in all samples | equalMedianNormalization |
| summarize peptide/PSM intensity into protein level relative abundance estimate by taking the median | medianSummary |
| summarize peptide/PSM intensity into protein level relative abundance estimate by median sweeping method | medianSweeping |
| summarize peptide/PSM intensity into protein level relative abundance estimate by Turkey median polish procedure | medpolishSummary |
| output the DEqMS analysis results in a data frame | outputResult |
| plot log2 intensities of all peptides for one gene in different samples | peptideProfilePlot |
| plot the residuals against the number of quantified peptides/PSMs. | Residualplot |
| Peptide/Spectra Count Based Empirical Bayes Statistics for Differential Expression | spectraCounteBayes |
| generate a boxplot of the variance | VarianceBoxplot |
| generate a scatter plot of the variance | VarianceScatterplot |
