Package: switchde 1.33.0
Kieran Campbell
switchde: Switch-like differential expression across single-cell trajectories
Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories.
Authors:
switchde_1.33.0.tar.gz
switchde_1.33.0.zip(r-4.5)switchde_1.33.0.zip(r-4.4)switchde_1.33.0.zip(r-4.3)
switchde_1.33.0.tgz(r-4.5-any)switchde_1.33.0.tgz(r-4.4-any)switchde_1.33.0.tgz(r-4.3-any)
switchde_1.33.0.tar.gz(r-4.5-noble)switchde_1.33.0.tar.gz(r-4.4-noble)
switchde_1.33.0.tgz(r-4.4-emscripten)switchde_1.33.0.tgz(r-4.3-emscripten)
switchde.pdf |switchde.html✨
switchde/json (API)
NEWS
| # Install 'switchde' in R: |
| install.packages('switchde', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kieranrcampbell/switchde/issues
- ex_pseudotime - Synthetic gene pseudotimes
- synth_gex - Synthetic gene expression matrix
On BioConductor:switchde-1.33.0(bioc 3.21)switchde-1.32.0(bioc 3.20)
immunooncologysoftwaretranscriptomicsgeneexpressionrnaseqregressiondifferentialexpressionsinglecellgene-expressiongenomicssingle-cell
Last updated 4 months agofrom:bf3d5a31bc. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 16 2025 |
| R-4.5-win | NOTE | Feb 16 2025 |
| R-4.5-mac | WARNING | Feb 16 2025 |
| R-4.5-linux | NOTE | Feb 16 2025 |
| R-4.4-win | NOTE | Feb 16 2025 |
| R-4.4-mac | NOTE | Feb 16 2025 |
| R-4.3-win | NOTE | Feb 16 2025 |
| R-4.3-mac | NOTE | Feb 16 2025 |
Exports:example_sigmoidextract_parsfit_nzi_modelfit_zi_modelswitchdeswitchplot
Dependencies:abindaskpassBiobaseBiocGenericsclicolorspacecrayoncurlDelayedArraydplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerrlangS4ArraysS4VectorsscalesSingleCellExperimentSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Synthetic gene pseudotimes | ex_pseudotime |
| Example sigmoid plot | example_sigmoid |
| Extract parameters from fitted model | extract_pars |
| Fit a (non-zero-inflated) model for a single gene | fit_nzi_model |
| Fit a zero-inflated model for a single gene | fit_zi_model |
| Switch-like model fitting and differential expression test | switchde |
| Plot gene behaviour | switchplot |
| Synthetic gene expression matrix | synth_gex |
