Installing ctsGE | Workflow of clustering with ctsGE | Building the expression matrix | Loading data from ncbi GEO | Loading data from files | Adding genes annotation to time series table | Defining the expression index | Index overview after | Clustering each index with K-means | Graphic visualization of an index | GUI for interactive exploration of gene-expression data | Screenshots of the GUI | The table tab
Package: ctsGE 1.39.0
Michal Sharabi-Schwager
ctsGE: Clustering of Time Series Gene Expression data
Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.
Authors:
ctsGE_1.39.0.tar.gz
ctsGE_1.39.0.zip(r-4.7)ctsGE_1.39.0.zip(r-4.6)ctsGE_1.39.0.zip(r-4.5)
ctsGE_1.39.0.tgz(r-4.6-any)ctsGE_1.39.0.tgz(r-4.5-any)
ctsGE_1.39.0.tar.gz(r-4.7-any)ctsGE_1.39.0.tar.gz(r-4.6-any)
ctsGE_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ctsGE/json (API)
| # Install 'ctsGE' in R: |
| install.packages('ctsGE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/michalsharabi/ctsge/issues
On BioConductor:ctsGE-1.39.0(bioc 3.24)ctsGE-1.38.0(bioc 3.23)
immunooncologygeneexpressiontranscriptiondifferentialexpressiongenesetenrichmentgeneticsbayesianclusteringtimecoursesequencingrnaseq
Last updated from:61143f9f76. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 174 | ||
| linux-devel-x86_64 | NOTE | 201 | ||
| source / vignettes | OK | 209 | ||
| linux-release-x86_64 | NOTE | 284 | ||
| macos-release-arm64 | NOTE | 108 | ||
| macos-oldrel-arm64 | NOTE | 130 | ||
| windows-devel | NOTE | 107 | ||
| windows-release | NOTE | 99 | ||
| windows-oldrel | NOTE | 120 | ||
| wasm-release | OK | 164 |
Exports:ClustIndexesctsGEShinyAppindexPlotIndexesClustPreparingTheIndexesreadTSGE
Dependencies:base64encbslibcachemccaPPclicommonmarkcpp11DEoptimRdigestfarverfastmapfontawesomefsggplot2gluegtablehtmltoolshttpuvisobandjquerylibjsonlitelabelinglaterlifecyclelimmamagrittrmemoisemimemvtnormotelpcaPPplyrpromisesR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangrobustbaseS7sassscalesshinysourcetoolsstatmodstringistringrvctrsviridisLitewithrxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clustering the indexes applying K-means | ClustIndexes |
| GUI for interactive exploration of gene expression data. | ctsGEShinyApp |
| Indexing function | index |
| Graphic visualization of an index | PlotIndexesClust |
| Define an expression index for each gene | PreparingTheIndexes |
| Read and merge a set of files containing gene expression data | readTSGE |
