{ "_id": "6a17df55acfb0bcc41d9d610", "Package": "DEqMS", "Version": "1.31.0", "Date": "2025/05/10", "Title": "a tool to perform statistical analysis of differential protein\nexpression for quantitative proteomics data.", "Author": "Yafeng Zhu", "Maintainer": "Yafeng Zhu ", "LazyLoad": "yes", "Description": "DEqMS is developped on top of Limma. However, Limma\nassumes same prior variance for all genes. In proteomics, the\naccuracy of protein abundance estimates varies by the number of\npeptides/PSMs quantified in both label-free and labelled data.\nProteins quantification by multiple peptides or PSMs are more\naccurate. DEqMS package is able to estimate different prior\nvariances for proteins quantified by different number of\nPSMs/peptides, therefore acchieving better accuracy. The\npackage can be applied to analyze both label-free and labelled\nproteomics data.", "License": "LGPL", "biocViews": "ImmunoOncology, Proteomics, MassSpectrometry, Preprocessing,\nDifferentialExpression,\nMultipleComparison,Normalization,Bayesian,ExperimentHubSoftware", "VignetteBuilder": "knitr", "Packaged": { "Date": "2026-05-28 06:19:14 UTC", "User": "root" }, "BugReports": "https://github.com/yafeng/DEqMS/issues", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:48:40 UTC", "RemoteUrl": "https://github.com/bioc/DEqMS", "RemoteRef": "HEAD", "RemoteSha": "fcec1ed7d05159dd822367a3adeab34193e32e8c", "NeedsCompilation": "no", "MD5sum": "1d2e7140a7ae20c5cf6d7461dfd4e7e7", "_user": "bioc", "_type": "src", "_file": "DEqMS_1.31.0.tar.gz", "_fileid": "184b6c030617f68614fb51bbc70ad575bf2e9ab7b16bcb8790d56df0615c6f41", "_filesize": 2325465, "_sha256": "184b6c030617f68614fb51bbc70ad575bf2e9ab7b16bcb8790d56df0615c6f41", "_created": "2026-05-28T06:19:14.000Z", 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"topics": [ "medianSweeping" ] }, { "page": "medpolishSummary", "title": "summarize peptide/PSM intensity into protein level relative abundance estimate by Turkey median polish procedure", "topics": [ "medpolishSummary" ] }, { "page": "outputResult", "title": "output the DEqMS analysis results in a data frame", "topics": [ "outputResult" ] }, { "page": "peptideProfilePlot", "title": "plot log2 intensities of all peptides for one gene in different samples", "topics": [ "peptideProfilePlot" ] }, { "page": "Residualplot", "title": "plot the residuals against the number of quantified peptides/PSMs.", "topics": [ "Residualplot" ] }, { "page": "spectraCounteBayes", "title": "Peptide/Spectra Count Based Empirical Bayes Statistics for Differential Expression", "topics": [ "spectraCounteBayes" ] }, { "page": "VarianceBoxplot", "title": "generate a boxplot of the variance", "topics": [ "VarianceBoxplot" ] }, { "page": "VarianceScatterplot", "title": "generate a scatter plot of the variance", "topics": [ "VarianceScatterplot" ] } ], "_readme": "https://github.com/bioc/DEqMS/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "limma", "magrittr", "matrixStats", "pillar", "pkgconfig", "R6", "RColorBrewer", "rlang", "S7", "scales", "statmod", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "DEqMS-package-vignette.Rmd", "filename": "DEqMS-package-vignette.html", "title": "DEqMS R Markdown vignettes", "author": "Yafeng Zhu, Lukas Orre, Yan Tran, Georgios Mermelekas, Henrik Johansson, Alina Malyutina, Simon Anders, Janne Lehtiö", "engine": "knitr::rmarkdown", "headings": [ "Overview of DEqMS", "Quick start", "Differential protein expression analysis with DEqMS using a protein table", "Download and Read the input protein table", "Extract quant data columns for DEqMS", "Make design table.", "Make contrasts", "DEqMS analysis", "Visualize the fit curve - variance dependence on quantified PSM", "Extract the results as a data frame and save it", "Make volcanoplot", "DEqMS analysis using MaxQuant outputs (label-free data)", "Read protein table as input and filter it", "Make a data frame of unique peptide count per protein", "DEqMS analysis on LFQ data", "Visualize the fit curve", "Extract outputs from DEqMS", "DEqMS analysis using a PSM table (isobaric labelled data)", "Read PSM table input", "Summarization and Normalization", "PSM/Peptide profile plot", "Comparing DEqMS to other methods", "Compare the variance estimate in DEqMS and Limma", "Prior variance comparison between DEqMS and Limma", "Residual plot for DEqMS and Limma", "Posterior variance comparison between DEqMS and Limma", "Compare p-values from DEqMS to ordinary t-test, ANOVA and Limma", "T-test analysis", "Anova analysis", "Limma", "Visualize the distribution of p-values by different analysis" ], "created": "2018-05-01 18:54:59", "modified": "2024-08-22 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