Introduction | Installation | Pre-filtering of genes | Example usage | Non-zero inflated | Zero-inflation | Controlling the EM algorithm | Use cases | Technical info
Package: switchde 1.39.0
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_1.39.0.tar.gz
switchde_1.39.0.zip(r-4.7-any)switchde_1.39.0.zip(r-4.6-any)switchde_1.39.0.zip(r-4.5-any)
switchde_1.39.0.tgz(r-4.6-any)switchde_1.39.0.tgz(r-4.5-any)
switchde_1.39.0.tar.gz(r-4.7-any)switchde_1.39.0.tar.gz(r-4.6-any)
switchde_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
switchde/json (API)
| # 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
Datasets:
- ex_pseudotime - Synthetic gene pseudotimes
- synth_gex - Synthetic gene expression matrix
On BioConductor:switchde-1.39.0(bioc 3.24)switchde-1.38.0(bioc 3.23)
immunooncologysoftwaretranscriptomicsgeneexpressionrnaseqregressiondifferentialexpressionsinglecellgene-expressiongenomicssingle-cell
Last updated from:8527700c44. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 190 | ||
| linux-devel | NOTE | 319 | ||
| source / vignettes | OK | 237 | ||
| linux-release | NOTE | 497 | ||
| macos-release | NOTE | 231 | ||
| macos-oldrel | NOTE | 200 | ||
| windows-devel | NOTE | 229 | ||
| windows-release | NOTE | 192 | ||
| windows-oldrel | NOTE | 192 | ||
| wasm-release | OK | 112 |
Exports:example_sigmoidextract_parsfit_nzi_modelfit_zi_modelswitchdeswitchplot
Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArraydplyrfarvergenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigR6RColorBrewerrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraySummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrXVector
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 |