Introduction | Data set and statistic testing on probe level | Incorporation of neighboring probes | Parameter estimation | Calculation of confidence intervals | Visualization | Exporting results to external software | Specification of custom weighting windows
Package: les 1.63.0
Julian Gehring
les: Identifying Differential Effects in Tiling Microarray Data
The 'les' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.
Authors:
les_1.63.0.tar.gz
les_1.63.0.zip(r-4.7)les_1.63.0.zip(r-4.6)les_1.63.0.zip(r-4.5)
les_1.63.0.tgz(r-4.6-any)les_1.63.0.tgz(r-4.5-any)
les_1.63.0.tar.gz(r-4.7-any)les_1.63.0.tar.gz(r-4.6-any)
les_1.63.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
les/json (API)
| # Install 'les' in R: |
| install.packages('les', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
On BioConductor:les-1.63.0(bioc 3.24)les-1.62.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarraydifferentialexpressionchipchipdnamethylationtranscription
Last updated from:6a07807bd6. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 130 | ||
| linux-devel-x86_64 | NOTE | 621 | ||
| source / vignettes | OK | 165 | ||
| linux-release-x86_64 | NOTE | 133 | ||
| macos-release-arm64 | NOTE | 93 | ||
| macos-oldrel-arm64 | NOTE | 138 | ||
| windows-devel | NOTE | 97 | ||
| windows-release | NOTE | 87 | ||
| windows-oldrel | NOTE | 87 | ||
| wasm-release | OK | 85 |
Exports:chi2ciepWeightestimateexportgaussWeightLesplotrectangWeightregionsshowsummarythresholdtriangWeight
Dependencies:bitopsbootcaToolsfdrtoolgplotsgtoolsKernSmoothRColorBrewer
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Identifying Differential Effects in Tiling Microarray Data | les-package les |
| chi2 | chi2 chi2,Les-method chi2-methods |
| ci | ci ci,Les ci,Les-method ci-methods |
| estimate | estimate estimate,Les-method estimate-methods |
| export | export export,Les export,Les-method export-methods |
| Class 'Les' | Les-class show,Les-method summary,Les-method [,Les-method [<-,Les-method |
| Les | Les Les,ANY,numeric-method Les-methods |
| plot method for class Les | plot plot,Les plot,Les-method plot-methods |
| regions | regions regions,Les regions,Les-method regions-methods |
| Spike-in ChIP-chip data set | exprs reference |
| Spike-in ChIP-chip data set | pos pval |
| threshold | threshold threshold,Les threshold,Les-method threshold-methods |
| Weighting functions | epWeight gaussWeight rectangWeight triangWeight weighting |