Package: DEqMS 1.25.0

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:Yafeng Zhu

DEqMS_1.25.0.tar.gz
DEqMS_1.25.0.zip(r-4.5)DEqMS_1.25.0.zip(r-4.4)DEqMS_1.25.0.zip(r-4.3)
DEqMS_1.25.0.tgz(r-4.5-any)DEqMS_1.25.0.tgz(r-4.4-any)DEqMS_1.25.0.tgz(r-4.3-any)
DEqMS_1.25.0.tar.gz(r-4.5-noble)DEqMS_1.25.0.tar.gz(r-4.4-noble)
DEqMS_1.25.0.tgz(r-4.4-emscripten)DEqMS_1.25.0.tgz(r-4.3-emscripten)
DEqMS.pdf |DEqMS.html
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-1.25.0(bioc 3.21)DEqMS-1.24.0(bioc 3.20)

immunooncologyproteomicsmassspectrometrypreprocessingdifferentialexpressionmultiplecomparisonnormalizationbayesianexperimenthubsoftwarelimmaquantitative-proteomic-analysis

8.18 score 23 stars 1 packages 58 scripts 477 downloads 3 mentions 10 exports 31 dependencies

Last updated 5 months agofrom:bdb1c603a0. Checks:1 OK, 8 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-winERRORMar 29 2025
R-4.5-macERRORMar 29 2025
R-4.5-linuxERRORMar 29 2025
R-4.4-winERRORMar 29 2025
R-4.4-macERRORMar 29 2025
R-4.4-linuxERRORMar 29 2025
R-4.3-winERRORMar 29 2025
R-4.3-macERRORMar 29 2025

Exports:equalMedianNormalizationmedianSummarymedianSweepingmedpolishSummaryoutputResultpeptideProfilePlotResidualplotspectraCounteBayesVarianceBoxplotVarianceScatterplot

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclelimmamagrittrMASSMatrixmatrixStatsmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalesstatmodtibbleutf8vctrsviridisLitewithr

DEqMS R Markdown vignettes

Rendered fromDEqMS-package-vignette.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2024-08-22
Started: 2018-05-01