switchde: Switch-like differential expression across single-cell trajectories

Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories.

Author
Kieran Campbell [aut, cre]
Date of publication
None
Maintainer
Kieran Campbell <kieranrcampbell@gmail.com>
License
GPL (>= 2)
Version
1.0.0
URLs

View on Bioconductor

Man pages

example_sigmoid
Example sigmoid plot
ex_pseudotime
Synthetic gene pseudotimes
extract_pars
Extract parameters from fitted model
fit_nzi_model
Fit a (non-zero-inflated) model for a single gene
fit_zi_model
Fit a zero-inflated model for a single gene
sanitise_inputs
Sanitise inputs for testDE and fitModel
sigmoid
Calculate the mean vector given parameters and pseudotimes...
switchde
Switch-like model fitting and differential expression test
switchplot
Plot gene behaviour
synth_gex
Synthetic gene expression matrix

Files in this package

switchde/DESCRIPTION
switchde/NAMESPACE
switchde/R
switchde/R/mle.R
switchde/R/switchde.R
switchde/R/zi.R
switchde/R/zi_constant.R
switchde/README.md
switchde/build
switchde/build/vignette.rds
switchde/data
switchde/data/ex_pseudotime.rda
switchde/data/synth_gex.rda
switchde/inst
switchde/inst/NEWS
switchde/inst/doc
switchde/inst/doc/switchde_vignette.R
switchde/inst/doc/switchde_vignette.Rmd
switchde/inst/doc/switchde_vignette.html
switchde/inst/example.png
switchde/inst/example_sigmoid.png
switchde/man
switchde/man/ex_pseudotime.Rd
switchde/man/example_sigmoid.Rd
switchde/man/extract_pars.Rd
switchde/man/fit_nzi_model.Rd
switchde/man/fit_zi_model.Rd
switchde/man/sanitise_inputs.Rd
switchde/man/sigmoid.Rd
switchde/man/switchde.Rd
switchde/man/switchplot.Rd
switchde/man/synth_gex.Rd
switchde/tests
switchde/tests/testthat
switchde/tests/testthat.R
switchde/tests/testthat/test_switchde.R
switchde/vignettes
switchde/vignettes/switchde_vignette.Rmd