Files in Linlab-slu/TSSr
TSS sequencing data analysis
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
Meta/vignette.rds
NAMESPACE
NEWS
R/Aclasses.R
R/Aexample.R
R/AnnotationFunctions.R
R/AnnotationMethods.R
R/ClusteringFunctions.R
R/ClusteringMethods.R
R/ConsensusFunctions.R
R/ConsensusMethods.R
R/EnhancerMethods.R
R/ExportFunctions.R
R/ExportMethods.R
R/ExpressionFunctions.R
R/ExpressionMethods.R
R/FilteringFunctions.R
R/FilteringMethods.R
R/ImportFunctions.R
R/ImportMethods.R
R/MergingMethods.R
R/NormalizationMethods.R
R/ShapeMethods.R
R/ShiftingFunctions.R
R/ShiftingMethods.R
R/TSSr.R
README.md
_pkgdown.yml
data/exampleTSSr.rda
doc/vignette.R
doc/vignette.Rmd
doc/vignette.html
docs/404.html
docs/LICENSE-text.html
docs/articles/figures/01_TSS_correlation_plot_of_all_samples.png
docs/articles/figures/02_PCA_plot.png
docs/articles/figures/03_Interquantile_plot_of_ALL_samples.png
docs/articles/figures/04_Shape_plot_of_ALL_samples.png
docs/articles/figures/05_Volcano_plot.png
docs/articles/figures/06_TSS_graphs.png
docs/articles/index.html
docs/articles/vignette.html
docs/articles/vignette_files/accessible-code-block-0.0.1/empty-anchor.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/ALL.samples.TSS.raw.txt
docs/reference/Interquantile_plot_of_ALL_samples.pdf
docs/reference/PCA_plot.pdf
docs/reference/Rplot001.png
docs/reference/Shape_plot_of_ALL_samples.pdf
docs/reference/TSS_correlation_plot_of_all_samples.pdf
docs/reference/TSSr-class.html
docs/reference/TSSr-package.html
docs/reference/Volcano_plot.pdf
docs/reference/annotateCluster.html
docs/reference/callEnhancer.html
docs/reference/clusterTSS.html
docs/reference/consensusCluster.html
docs/reference/control.TSS.processed.minus.bedGraph
docs/reference/control.TSS.processed.plus.bedGraph
docs/reference/control.assignedClusters.txt
docs/reference/control.consensusClusters.txt
docs/reference/control.filteredClusters.txt
docs/reference/control.promoter.shape.txt
docs/reference/control.tagClusters.txt
docs/reference/control.unassignedClusters.txt
docs/reference/control_VS_treat.DE.table.sig.txt
docs/reference/control_VS_treat.promoter.shift.table.txt
docs/reference/deGene.html
docs/reference/exampleTSSr.html
docs/reference/exportClustersTable.html
docs/reference/exportClustersToBed.html
docs/reference/exportDETable.html
docs/reference/exportEnhancerTable.html
docs/reference/exportShapeTable.html
docs/reference/exportShiftTable.html
docs/reference/exportTSStable.html
docs/reference/exportTSStoBedgraph.html
docs/reference/filterTSS.html
docs/reference/getTSS.html
docs/reference/index.html
docs/reference/mergeSamples.html
docs/reference/normalizeTSS.html
docs/reference/plotCorrelation.html
docs/reference/plotDE.html
docs/reference/plotInterQuantile.html
docs/reference/plotShape.html
docs/reference/plotTSS.html
docs/reference/plotTssPCA.html
docs/reference/shapeCluster.html
docs/reference/shiftPromoter.html
docs/reference/treat.TSS.processed.minus.bedGraph
docs/reference/treat.TSS.processed.plus.bedGraph
docs/reference/treat.assignedClusters.txt
docs/reference/treat.consensusClusters.txt
docs/reference/treat.filteredClusters.txt
docs/reference/treat.promoter.shape.txt
docs/reference/treat.tagClusters.txt
docs/reference/treat.unassignedClusters.txt
inst/CITATION
man/TSSr-class.Rd
man/TSSr-package.Rd
man/annotateCluster.Rd
man/callEnhancer.Rd
man/clusterTSS.Rd
man/consensusCluster.Rd
man/deGene.Rd
man/exampleTSSr.Rd
man/exportClustersTable.Rd
man/exportClustersToBed.Rd
man/exportDETable.Rd
man/exportEnhancerTable.Rd
man/exportShapeTable.Rd
man/exportShiftTable.Rd
man/exportTSStable.Rd
man/exportTSStoBedgraph.Rd
man/filterTSS.Rd
man/getTSS.Rd
man/mergeSamples.Rd
man/normalizeTSS.Rd
man/plotCorrelation.Rd
man/plotDE.Rd
man/plotInterQuantile.Rd
man/plotShape.Rd
man/plotTSS.Rd
man/plotTssPCA.Rd
man/shapeCluster.Rd
man/shiftPromoter.Rd
tssr.yml
vignettes/figures/01_TSS_correlation_plot_of_all_samples_v2.png
vignettes/figures/02_PCA_plot_v2.png
vignettes/figures/02_PCA_plot_v3.png
vignettes/figures/03_Interquantile_plot_of_ALL_samples_v2.png
vignettes/figures/04_Shape_plot_of_ALL_samples_v2.png
vignettes/figures/05_Volcano_plot_v2.png
vignettes/figures/06_TSS_graphs_v3.png
vignettes/figures/TSSr_flowchart.png
vignettes/vignette.Rmd
