Package: PepSetTest 1.1.0
Junmin Wang
PepSetTest: Peptide Set Test
Peptide Set Test (PepSetTest) is a peptide-centric strategy to infer differentially expressed proteins in LC-MS/MS proteomics data. This test detects coordinated changes in the expression of peptides originating from the same protein and compares these changes against the rest of the peptidome. Compared to traditional aggregation-based approaches, the peptide set test demonstrates improved statistical power, yet controlling the Type I error rate correctly in most cases. This test can be valuable for discovering novel biomarkers and prioritizing drug targets, especially when the direct application of statistical analysis to protein data fails to provide substantial insights.
Authors:
PepSetTest_1.1.0.tar.gz
PepSetTest_1.1.0.zip(r-4.5)PepSetTest_1.1.0.zip(r-4.4)PepSetTest_1.1.0.zip(r-4.3)
PepSetTest_1.1.0.tgz(r-4.5-any)PepSetTest_1.1.0.tgz(r-4.4-any)PepSetTest_1.1.0.tgz(r-4.3-any)
PepSetTest_1.1.0.tar.gz(r-4.5-noble)PepSetTest_1.1.0.tar.gz(r-4.4-noble)
PepSetTest_1.1.0.tgz(r-4.4-emscripten)PepSetTest_1.1.0.tgz(r-4.3-emscripten)
PepSetTest.pdf |PepSetTest.html✨
PepSetTest/json (API)
| # Install 'PepSetTest' in R: |
| install.packages('PepSetTest', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jmwangbio/pepsettest/issues
On BioConductor:PepSetTest-1.1.0(bioc 3.21)PepSetTest-1.0.0(bioc 3.20)
differentialexpressionregressionproteomicsmassspectrometry
Last updated 4 months agofrom:7d3c75f760. Checks:5 OK, 3 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 28 2025 |
| R-4.5-win | NOTE | Jan 28 2025 |
| R-4.5-mac | NOTE | Jan 28 2025 |
| R-4.5-linux | NOTE | Jan 28 2025 |
| R-4.4-win | OK | Jan 28 2025 |
| R-4.4-mac | OK | Jan 28 2025 |
| R-4.3-win | OK | Jan 28 2025 |
| R-4.3-mac | OK | Jan 28 2025 |
Exports:AggLimmaWorkflowAggPepsCompPepSetTestCompPepSetTestWorkflowEnframeContrastsResEstimInterPepCorFitContrastsFitLmerBySampleRobustRegSelfContPepSetTestWorkflowTTestwCor
Dependencies:abindaskpassBiobaseBiocGenericsbootclicrayoncurlDelayedArraydplyrfansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelatticelifecyclelimmalme4magrittrMASSMatrixMatrixGenericsmatrixStatsmimeminqanlmenloptropensslpillarpkgconfigplyrR6rbibutilsRcppRcppEigenRdpackreformulasreshape2rlangS4ArraysS4VectorsSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrswithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregation-based LIMMA workflow | AggLimmaWorkflow |
| Aggregate peptide abundance values | AggPeps |
| Competitive peptide set test | CompPepSetTest |
| Competitive Peptide Set Test Workflow | CompPepSetTestWorkflow |
| Enframe result of LIMMA analysis | EnframeContrastsRes |
| Estimation of inter-peptide correlation | EstimInterPepCor |
| Empirical Bayes moderated t-test | FitContrasts |
| Fit a linear mixed model | FitLmerBySample |
| Robust Regression | RobustReg |
| Self-contained Peptide Set Test Workflow | SelfContPepSetTestWorkflow |
| Two-sample t-test accounting for inter-peptide correlation | TTestwCor |
