SEPA: SEPA

Given single-cell RNA-seq data and true experiment time of cells or pseudo-time cell ordering, SEPA provides convenient functions for users to assign genes into different gene expression patterns such as constant, monotone increasing and increasing then decreasing. SEPA then performs GO enrichment analysis to analysis the functional roles of genes with same or similar patterns.

AuthorZhicheng Ji, Hongkai Ji
Date of publicationNone
MaintainerZhicheng Ji <zji4@jhu.edu>
LicenseGPL(>=2)
Version1.4.0

View on Bioconductor

Files

SEPA/DESCRIPTION
SEPA/NAMESPACE
SEPA/R
SEPA/R/HSMMdata.R SEPA/R/SEPA.R SEPA/R/SEPAui.R SEPA/R/patternGOanalysis.R SEPA/R/patternsummary.R SEPA/R/pseudotime.R SEPA/R/pseudotimepattern.R SEPA/R/pseudotimevisualize.R SEPA/R/truetime.R SEPA/R/truetimepattern.R SEPA/R/truetimevisualize.R SEPA/R/windowGOanalysis.R SEPA/R/windowGOvisualize.R
SEPA/README.md
SEPA/build
SEPA/build/vignette.rds
SEPA/data
SEPA/data/HSMMdata.rda
SEPA/inst
SEPA/inst/doc
SEPA/inst/doc/SEPA.R
SEPA/inst/doc/SEPA.Rnw
SEPA/inst/doc/SEPA.pdf
SEPA/inst/shiny
SEPA/inst/shiny/server.R
SEPA/inst/shiny/shinyapps
SEPA/inst/shiny/shinyapps/zhiji
SEPA/inst/shiny/shinyapps/zhiji/SEPA.dcf
SEPA/inst/shiny/ui.R
SEPA/inst/shiny/www
SEPA/inst/shiny/www/ajaxloaderq.gif
SEPA/inst/shiny/www/busy.js
SEPA/inst/shiny/www/style.css
SEPA/man
SEPA/man/HSMMdata.Rd SEPA/man/SEPA.Rd SEPA/man/SEPAui.Rd SEPA/man/patternGOanalysis.Rd SEPA/man/patternsummary.Rd SEPA/man/pseudotime.Rd SEPA/man/pseudotimepattern.Rd SEPA/man/pseudotimevisualize.Rd SEPA/man/truetime.Rd SEPA/man/truetimepattern.Rd SEPA/man/truetimevisualize.Rd SEPA/man/windowGOanalysis.Rd SEPA/man/windowGOvisualize.Rd
SEPA/vignettes
SEPA/vignettes/SEPA.Rnw

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