Files in shbrief/GenomicSuperSignature
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
.Rbuildignore
.github/workflows/check-and-test.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/GenomicSignatures-class.R
R/GenomicSignatures-methods.R
R/PCAGenomicSignatures-methods.R
R/annotatePC.R
R/annotateRAV.R
R/availableRAVmodel.R
R/buildAvgLoading.R
R/calculateScore.R
R/data.R
R/drawWordcloud.R
R/extractPC.R
R/findSignature.R
R/findStudiesInCluster.R
R/getMetadata.R
R/getModel.R
R/heatmapTable.R
R/plotAnnotatedPCA.R
R/plotValidate.R
R/rmNaInf.R
R/sampleScoreHeatmap.R
R/subsetEnrichedPathways.R
R/utils.R
R/validate.R
R/validatedSignatures.R
README.md
_pkgdown.yml
data-raw/droplist.R
data-raw/filterList.R
data-raw/miniRAVmodel.R
data/droplist.RData
data/filterList.RData
data/miniAllZ.rda
data/miniRAVmodel.RData
data/miniTCGA.rda
data/res_hcut.rda
inst/CITATION
inst/extdata/README.md
inst/extdata/availableRAVmodel.csv
inst/extdata/studyMeta.tsv.gz
inst/scripts/funcForGSEA_plot.R
inst/scripts/gss.R
inst/scripts/gss.Rmd
inst/scripts/searchPathways.R
man/GenomicSignatures-class.Rd
man/GenomicSignatures-methods.Rd
man/PCAGenomicSignatures-class.Rd
man/PCAGenomicSignatures-methods.Rd
man/PCAGenomicSignatures.Rd
man/PCinRAV.Rd
man/annotatePC.Rd
man/annotateRAV.Rd
man/availableRAVmodel.Rd
man/buildAvgLoading.Rd
man/calculateScore.Rd
man/dot-RAVName.Rd
man/dot-calculateSilhouetteWidth.Rd
man/dot-loadingCor.Rd
man/drawWordcloud.Rd
man/droplist.Rd
man/extractPC.Rd
man/filterList.Rd
man/findKeywordInRAV.Rd
man/findSignature.Rd
man/findStudiesInCluster.Rd
man/getModel.Rd
man/getRAVInfo.Rd
man/getStudyInfo.Rd
man/heatmapTable.Rd
man/meshTable.Rd
man/miniAllZ.Rd
man/miniRAVmodel.Rd
man/miniTCGA.Rd
man/plotAnnotatedPCA.Rd
man/plotValidate.Rd
man/res_hcut.Rd
man/rmNaInf.Rd
man/sampleScoreHeatmap.Rd
man/subsetEnrichedPathways.Rd
man/validate.Rd
man/validatedSignatures.Rd
tests/testthat.R
tests/testthat/microTCGA.rds
tests/testthat/test-annotatePC.R
tests/testthat/test-annotateRAV.R
tests/testthat/test-calculateScore.R
tests/testthat/test-drawWordcloud.R
tests/testthat/test-findSignature.R
tests/testthat/test-findStudiesInCluster.R
tests/testthat/test-getMetadata.R
tests/testthat/test-subsetEnrichedPathways.R
tests/testthat/test-validate.R
tests/testthat/test-validatedSignatures.R
update.sh
vignettes/Contents.Rmd
vignettes/GSig_model_buildling_diagram.png
vignettes/GSig_model_usage_diagram.png
vignettes/GSig_overview.png
vignettes/Quickstart.Rmd
