Package: conformeR 0.99.1

Justine Leclerc
conformeR: Conformalized differential expression analysis of multi-condition single-cell data
conformeR provides conformal prediction layers for the cell neighborhood construction step of the LEMUR framework. It implements two complementary approaches, conformal clustering and conformal selection, to quantify uncertainty in the resulting cell neighborhoods, together with tools for visualizing and interpreting the resulting uncertainty sets.
Authors:
conformeR_0.99.1.tar.gz
conformeR_0.99.1.zip(r-4.7-any)conformeR_0.99.1.zip(r-4.6-any)conformeR_0.99.1.zip(r-4.5-any)
conformeR_0.99.1.tgz(r-4.6-any)conformeR_0.99.1.tgz(r-4.5-any)
conformeR_0.99.1.tar.gz(r-4.7-any)conformeR_0.99.1.tar.gz(r-4.6-any)
conformeR_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
conformeR/json (API)
| # Install 'conformeR' in R: |
| install.packages('conformeR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/juslecl/conformer/issues
- sce_reduced - Example single-cell dataset
transcriptomicsdifferentialexpressionsinglecelldimensionreductionclassificationclusteringvisualizationgeneexpressiongenepredictiongenetarget
Last updated from:87cc23ed1c. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 163 | ||
| linux-devel | OK | 258 | ||
| source / vignettes | OK | 432 | ||
| linux-release | OK | 248 | ||
| macos-release | OK | 196 | ||
| macos-oldrel | OK | 198 | ||
| windows-devel | OK | 231 | ||
| windows-release | OK | 255 | ||
| windows-oldrel | OK | 247 | ||
| wasm-release | OK | 146 |
Exports:conformeRplotter_conformal_clusteringplotter_conformal_selection
Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsbiocmakeBiocNeighborsBiocParallelclicodetoolscowplotcpp11DelayedArrayDelayedMatrixStatsdigestdir.expirydplyrdqrngfarverfilelockFNNformatRfurrrfutile.loggerfutile.optionsfuturegenericsGenomicRangesggnewscaleggplot2glmGamPoiglobalsgluegtableh5mreadHDF5ArrayIRangesirlbaisobandlabelinglambda.rlatticelemurlifecyclelimmalistenvmagrittrMatrixMatrixGenericsmatrixStatsparallellypillarpkgconfigpurrrR6RColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressrhdf5rhdf5filtersRhdf5librlangrsampleRSpectraS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsitmoslidersnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimenttibbletidyrtidyselectutf8uwotvctrsviridisLitewarpwithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| LEMUR analysis for neighborhoods on predicted gene differential expression with conformal methods | conformeR |
| Plot conformal clustering results on the LEMUR embedding | plotter_conformal_clustering |
| Plot conformal selection results on the LEMUR embedding | plotter_conformal_selection |
| Example single-cell dataset | sce_reduced |
