Package: Cepo 1.19.0
Hani Jieun Kim
Cepo: Cepo for the identification of differentially stable genes
Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.
Authors:
Cepo_1.19.0.tar.gz
Cepo_1.19.0.zip(r-4.7)Cepo_1.19.0.zip(r-4.6)Cepo_1.19.0.zip(r-4.5)
Cepo_1.19.0.tgz(r-4.6-any)Cepo_1.19.0.tgz(r-4.5-any)
Cepo_1.19.0.tar.gz(r-4.7-any)Cepo_1.19.0.tar.gz(r-4.6-any)
Cepo_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Cepo/json (API)
NEWS
| # Install 'Cepo' in R: |
| install.packages('Cepo', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- cellbench - Cellbench
- sce_pancreas - Sce_pancreas
On BioConductor:Cepo-1.19.0(bioc 3.24)Cepo-1.18.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
classificationgeneexpressionsinglecellsoftwaresequencingdifferentialexpression
Last updated from:5f662d15b8. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 238 | ||
| linux-devel-x86_64 | WARNING | 458 | ||
| source / vignettes | ERROR | 380 | ||
| linux-release-x86_64 | WARNING | 398 | ||
| macos-release-arm64 | WARNING | 312 | ||
| macos-oldrel-arm64 | WARNING | 202 | ||
| windows-devel | WARNING | 354 | ||
| windows-release | WARNING | 329 | ||
| windows-oldrel | WARNING | 406 | ||
| wasm-release | OK | 187 |
Exports:CepoplotDensitiestopGenes
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsbiocmakeBiocParallelBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayDelayedMatrixStatsdir.expirydplyrfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegraphGSEABasegtableh5mreadHDF5ArrayhttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpatchworkpillarpkgconfigplyrpngpurrrR6RColorBrewerRcppreshape2rhdf5rhdf5filtersRhdf5librlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsystibbletidyselectutf8vctrsviridisLitewithrXMLxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| cellbench | cellbench |
| Computing Cepo cell identity genes | Cepo |
| Plot densities | plotDensities |
| sce_pancreas | sce_pancreas |
| Setting parallel params based on operating platform | setCepoBPPARAM |
| Extract the top genes from the Cepo output | topGenes |
