SEPA: SEPA

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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.

Author
Zhicheng Ji, Hongkai Ji
Date of publication
None
Maintainer
Zhicheng Ji <zji4@jhu.edu>
License
GPL(>=2)
Version
1.4.0

View on Bioconductor

Man pages

HSMMdata
Sinlge-cell RNA-seq data for HSMM (Human Skeletal Muscle...
patternGOanalysis
patternGOanalysis
patternsummary
patternsummary
pseudotime
Pseudo-time Cell Ordering for HSMM Sinlge-cell RNA-seq data
pseudotimepattern
pseudotimepattern
pseudotimevisualize
pseudotimevisualize
SEPA
SEPA: Single-Cell Gene Expression Pattern Analysis
SEPAui
SEPAui
truetime
True Experiment Time Points for HSMM Sinlge-cell RNA-seq data
truetimepattern
truetimepattern
truetimevisualize
truetimevisualize
windowGOanalysis
windowGOanalysis
windowGOvisualize
windowGOvisualize

Files in this package

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