Package: Cepo 1.13.0
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_1.13.0.tar.gz
Cepo_1.13.0.zip(r-4.5)Cepo_1.13.0.zip(r-4.4)Cepo_1.13.0.zip(r-4.3)
Cepo_1.13.0.tgz(r-4.4-any)Cepo_1.13.0.tgz(r-4.3-any)
Cepo_1.13.0.tar.gz(r-4.5-noble)Cepo_1.13.0.tar.gz(r-4.4-noble)
Cepo_1.13.0.tgz(r-4.4-emscripten)Cepo_1.13.0.tgz(r-4.3-emscripten)
Cepo.pdf |Cepo.html✨
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-1.13.0(bioc 3.21)Cepo-1.12.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
classificationgeneexpressionsinglecellsoftwaresequencingdifferentialexpression
Last updated 2 months agofrom:5cb935f5d1. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:CepoplotDensitiestopGenes
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArrayDelayedMatrixStatsdplyrfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegraphGSEABasegtableHDF5ArrayhttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrplyrpngpurrrR6RColorBrewerRcppreshape2rhdf5rhdf5filtersRhdf5librlangRSQLiteS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectorzlibbioc
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 |
