Files in CityUHK-CompBio/HTSanalyzeR2
HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data
.Rbuildignore
.gitignore
DESCRIPTION
HTSanalyzeR2.Rproj
NAMESPACE
R/Batch_class.R
R/HTSanalyzeR2.R
R/HTSanalyzeR2Pipe.R
R/HTSanalyzeR4MAGeCK.R
R/RcppExports.R
R/accessor.R
R/class_union.R
R/d3plot.R
R/data.R
R/gscaTS.R
R/gsca_analyze.R
R/gsca_class.R
R/gsca_enrichmap.R
R/gsca_load_genesets.R
R/gsca_preprocess.R
R/gsca_report.R
R/gsca_summarize.R
R/gsca_view.R
R/nwaTS.R
R/nwa_analyze.R
R/nwa_class.R
R/nwa_preprocess.R
R/nwa_report.R
R/nwa_summarize.R
R/nwa_view.R
R/stat_test.R
R/sysdata.rda
R/utils.R
R/zzz.R
README.md
data/Biogrid_HS_Interactome.rda
data/Biogrid_HS_Mat.rda
data/GSE33113_exp.rda
data/GSE33113_label.rda
data/GSE33113_limma.rda
data/d13.rda
data/d25.rda
data/d7.rda
data/d7_gsca.rda
data/d7_nwa.rda
data/gscaTS.rda
data/nwaTS.rda
data/xn.rda
inst/NEWS
inst/htmlwidgets/forceGraph.js
inst/htmlwidgets/forceGraph.yaml
inst/htmlwidgets/forceGraph/common.css
inst/htmlwidgets/forceGraph/common.js
inst/htmlwidgets/forceGraph/jquery.min.js
inst/htmlwidgets/forceGraph/plugins.min.js
inst/htmlwidgets/forceGraph/settings.js
inst/htmlwidgets/forceGraph/sigma.min.js
inst/templates/app.R
inst/templates/settings.html
man/Biogrid_HS_Interactome.Rd
man/Biogrid_HS_Mat.Rd
man/GOGeneSets.Rd
man/GSCA.Rd
man/GSCABatch.Rd
man/GSE33113_exp.Rd
man/GSE33113_label.Rd
man/GSE33113_limma.Rd
man/HTSanalyzeR2.Rd
man/HTSanalyzeR2Pipe.Rd
man/HTSanalyzeR4MAGeCK.Rd
man/KeggGeneSets.Rd
man/MSigDBGeneSets.Rd
man/NWA.Rd
man/NWABatch.Rd
man/analyze.Rd
man/analyzeGscaTS.Rd
man/analyzeNwaTS.Rd
man/annotationConvertor.Rd
man/appendGSTerms.Rd
man/appendGSTermsTS.Rd
man/cellHTS2OutputStatTests.Rd
man/d7.Rd
man/d7_gsca.Rd
man/d7_nwa.Rd
man/duplicateRemover.Rd
man/extractEnrichMap-GSCA-method.Rd
man/extractSubNet-NWA-method.Rd
man/forceGraph.Rd
man/getInteractome.Rd
man/getPara.Rd
man/getResult.Rd
man/getSummary.Rd
man/getTopGeneSets.Rd
man/gscaTS.Rd
man/interactome.Rd
man/interactomeNwaTS.Rd
man/nwaTS.Rd
man/plotGSEA.Rd
man/preprocess.Rd
man/preprocessGscaTS.Rd
man/preprocessNwaTS.Rd
man/report.Rd
man/reportAll.Rd
man/summarize.Rd
man/viewEnrichMap-GSCA-method.Rd
man/viewGSEA.Rd
man/viewSubNet-NWA-method.Rd
man/xn.Rd
src/.gitignore
src/RcppExports.cpp
src/calcGScore.cpp
src/symbols.rds
vignettes/HTSanalyzeR2-vignette.Rmd
vignettes/HTSanalyzeR2-vignette.pdf
vignettes/Interactive-Shiny-report-of-HTSanalyzeR2.Rmd
vignettes/Interactive-Shiny-report-of-HTSanalyzeR2.pdf
vignettes/bibliography.bib
vignettes/figures/1.PNG
vignettes/figures/2.PNG
vignettes/figures/3.PNG
vignettes/figures/4.PNG
vignettes/figures/5.PNG
vignettes/figures/6.PNG
vignettes/figures/7.PNG
vignettes/figures/GSEAplot1.png
vignettes/figures/GSEAplot2.png
vignettes/figures/enrichmentMap1.PNG
vignettes/figures/enrichmentMap2.PNG
vignettes/figures/enrichmentMap3.PNG
vignettes/figures/enrichmentMap4.PNG
vignettes/figures/enrichmentMap5.png
vignettes/figures/enrichmentMap6.png
vignettes/figures/enrichmentMap7.png
vignettes/figures/enrichmentMap8.png
vignettes/figures/readme.example1.png
vignettes/figures/readme.example2.png
vignettes/figures/shinyReport1.PNG
vignettes/figures/shinyReport2.PNG
vignettes/figures/shinyReport3.PNG
vignettes/figures/subnetwork1.PNG
vignettes/figures/workFlow.png
