Metrics which estimate similarity between two ChIP-Seq profiles | Introduction | Loading the similaRpeak package | Inputs | ChIP-Seq profiles vectors | Metrics | Metric versus Pseudometric | Metrics Presentation | RATIO_AREA | DIFF_POS_MAX | RATIO_MAX_MAX | RATIO_INTERSECT | RATIO_NORMALIZED_INTERSECT | SPEARMAN_CORRELATION | Using similaRpeak on real ChIP-Seq profiles | Metrics calculation using a MetricFactory object | Session info | References
Package: similaRpeak 1.45.0
Astrid Deschênes
similaRpeak: Metrics to estimate a level of similarity between two ChIP-Seq profiles
This package calculates metrics which quantify the level of similarity between ChIP-Seq profiles. More specifically, the package implements six pseudometrics specialized in pattern similarity detection in ChIP-Seq profiles.
Authors:
similaRpeak_1.45.0.tar.gz
similaRpeak_1.45.0.zip(r-4.7)similaRpeak_1.45.0.zip(r-4.6)similaRpeak_1.45.0.zip(r-4.5)
similaRpeak_1.45.0.tgz(r-4.6-any)similaRpeak_1.45.0.tgz(r-4.5-any)
similaRpeak_1.45.0.tar.gz(r-4.7-any)similaRpeak_1.45.0.tar.gz(r-4.6-any)
similaRpeak_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
similaRpeak/json (API)
| # Install 'similaRpeak' in R: |
| install.packages('similaRpeak', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/adeschen/similarpeak/issues
Datasets:
- chr7Profiles - ChIP-Seq profiles of region chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1
- demoProfiles - ChIP-Seq profiles of region chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1
On BioConductor:similaRpeak-1.45.0(bioc 3.24)similaRpeak-1.44.0(bioc 3.23)
biologicalquestionchipseqgeneticsmultiplecomparisondifferentialexpressionbioconductorbioconductor-packagechip-profileschip-seqmetrics
Last updated from:20d8eb7b4c. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 132 | ||
| linux-devel-x86_64 | NOTE | 170 | ||
| source / vignettes | OK | 220 | ||
| linux-release-x86_64 | NOTE | 176 | ||
| macos-release-arm64 | NOTE | 89 | ||
| macos-oldrel-arm64 | NOTE | 96 | ||
| windows-devel | NOTE | 137 | ||
| windows-release | NOTE | 101 | ||
| windows-oldrel | NOTE | 100 | ||
| wasm-release | OK | 116 |
Exports:MetricFactorysimilarity
Dependencies:R6
