switchde: Switch-like differential expression across single-cell trajectories
Version 1.2.0

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

Browse man pages Browse package API and functions Browse package files

AuthorKieran Campbell [aut, cre]
Bioconductor views DifferentialExpression GeneExpression RNASeq Regression Software Transcriptomics
Date of publicationNone
MaintainerKieran Campbell <kieranrcampbell@gmail.com>
LicenseGPL (>= 2)
Version1.2.0
URL https://github.com/kieranrcampbell/switchde
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("switchde")

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
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

Functions

EM_constant Source code
EM_sigmoid Source code
Q_constant Source code
Q_grad_constant Source code
Q_grad_sigmoid Source code
Q_sigmoid Source code
constant_E_step Source code
ex_pseudotime Man page
example_sigmoid Man page Source code
extract_pars Man page Source code
fit_constant_model Source code
fit_nzi_model Man page Source code
fit_sigmoidal_model Source code
fit_zi_model Man page Source code
grad_likelihood_sigmoidal Source code
likelihood_constant Source code
likelihood_sigmoidal Source code
logDiffExp Source code Source code
sanitise_inputs Man page Source code
sigmoid Man page Source code
sigmoid_E_step Source code
switchde Man page Source code
switchplot Man page Source code
synth_gex Man page

Files

DESCRIPTION
NAMESPACE
R
R/mle.R
R/switchde.R
R/zi.R
R/zi_constant.R
README.md
build
build/vignette.rds
data
data/ex_pseudotime.rda
data/synth_gex.rda
inst
inst/NEWS
inst/doc
inst/doc/switchde_vignette.R
inst/doc/switchde_vignette.Rmd
inst/doc/switchde_vignette.html
inst/example.png
inst/example_sigmoid.png
man
man/ex_pseudotime.Rd
man/example_sigmoid.Rd
man/extract_pars.Rd
man/fit_nzi_model.Rd
man/fit_zi_model.Rd
man/sanitise_inputs.Rd
man/sigmoid.Rd
man/switchde.Rd
man/switchplot.Rd
man/synth_gex.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_switchde.R
vignettes
vignettes/switchde_vignette.Rmd
switchde documentation built on May 20, 2017, 10:38 p.m.