Introduction | 1. Environment Setup and Data Preparation | 2. Importing MSigDB Signatures and Scoring | 3. Computing the Convergence Score | 4. Visualization | Proportion Barplot | Crossed Proportion Barplot | Density Distribution | 5. Statistical Testing | Bivariate Test | Multivariate Linear Model | 6. Working with Seurat Objects | Session Information
Package: ConvergeR 0.99.2
ConvergeR: Whitfield Convergence Score and Seurat Metadata Association
Calculates the convergence score defined by Whitfield et al. 2026 <doi:10.1158/0008-5472.CAN-25-4403>. It allows visualization of this score alongside qualitative and quantitative Seurat object metadata via barplots and density curves, and runs appropriate statistical tests for associations. The code was built, corrected and adapted to SingleCellExpriment with the help of Gemini.
Authors:
ConvergeR_0.99.2.tar.gz
ConvergeR_0.99.2.zip(r-4.7-any)ConvergeR_0.99.2.zip(r-4.6-any)ConvergeR_0.99.2.zip(r-4.5-any)
ConvergeR_0.99.2.tgz(r-4.6-any)ConvergeR_0.99.2.tgz(r-4.5-any)
ConvergeR_0.99.2.tar.gz(r-4.7-any)ConvergeR_0.99.2.tar.gz(r-4.6-any)
ConvergeR_0.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ConvergeR/json (API)
| # Install 'ConvergeR' in R: |
| install.packages('ConvergeR', repos = c('https://pauldeboissier1.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pauldeboissier1/converger/issues
softwaresinglecelltranscriptomicsgeneexpression
Last updated from:fb0f2ff8e7. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 361 | ||
| source / vignettes | OK | 337 | ||
| linux-release | NOTE | 394 | ||
| macos-release | NOTE | 310 | ||
| macos-oldrel | NOTE | 376 | ||
| windows-devel | NOTE | 293 | ||
| windows-release | NOTE | 307 | ||
| windows-oldrel | NOTE | 289 | ||
| wasm-release | OK | 180 |
Exports:CalculateConvergedScorePlotConvergenceCrossedProportionPlotConvergenceDensityPlotConvergenceProportionTestConvergenceScoreTestMultivariateConvergence
Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsbitopsbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tableDelayedArraydeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppThreadRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS4ArraysS4VectorsS7sassscalesscattermoresctransformSeqinfoSeuratSeuratObjectshinySingleCellExperimentsitmosourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate Converged Score | CalculateConvergedScore |
| Plot Convergence Crossed Proportion | PlotConvergenceCrossedProportion |
| Plot Convergence Density | PlotConvergenceDensity |
| Plot Convergence Proportion | PlotConvergenceProportion |
| Test Convergence Score | TestConvergenceScore |
| Test Multivariate Convergence | TestMultivariateConvergence |