Package: CNVMetrics 1.11.0
Astrid Deschênes
CNVMetrics: Copy Number Variant Metrics
The CNVMetrics package calculates similarity metrics to facilitate copy number variant comparison among samples and/or methods. Similarity metrics can be employed to compare CNV profiles of genetically unrelated samples as well as those with a common genetic background. Some metrics are based on the shared amplified/deleted regions while other metrics rely on the level of amplification/deletion. The data type used as input is a plain text file containing the genomic position of the copy number variations, as well as the status and/or the log2 ratio values. Finally, a visualization tool is provided to explore resulting metrics.
Authors:
CNVMetrics_1.11.0.tar.gz
CNVMetrics_1.11.0.zip(r-4.5)CNVMetrics_1.11.0.zip(r-4.4)CNVMetrics_1.11.0.zip(r-4.3)
CNVMetrics_1.11.0.tgz(r-4.4-any)CNVMetrics_1.11.0.tgz(r-4.3-any)
CNVMetrics_1.11.0.tar.gz(r-4.5-noble)CNVMetrics_1.11.0.tar.gz(r-4.4-noble)
CNVMetrics_1.11.0.tgz(r-4.4-emscripten)CNVMetrics_1.11.0.tgz(r-4.3-emscripten)
CNVMetrics.pdf |CNVMetrics.html✨
CNVMetrics/json (API)
NEWS
| # Install 'CNVMetrics' in R: |
| install.packages('CNVMetrics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/krasnitzlab/cnvmetrics/issues
On BioConductor:CNVMetrics-1.9.0(bioc 3.20)CNVMetrics-1.8.0(bioc 3.19)
biologicalquestionsoftwarecopynumbervariationcnvcopy-number-variationmetricsr-language
Last updated 23 days agofrom:961ad8c8c0. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | OK | Oct 30 2024 |
| R-4.3-mac | OK | Oct 30 2024 |
Exports:calculateLog2ratioMetriccalculateOverlapMetricplotMetricprocessSim
Dependencies:askpassBHBiocGenericsBiocParallelclicodetoolscolorspacecpp11curlfarverformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluegridExtragtablehttrIRangesjsonlitelabelinglambda.rlifecyclemagrittrmimemunsellopensslpheatmapR6rBeta2009RColorBrewerrlangS4VectorsscalessnowsysUCSC.utilsviridisLiteXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CNVMetrics: Copy number variant metrics | CNVMetrics-package CNVMetrics |
| Calculate metric using overlapping amplified/deleted regions | calculateLog2ratioMetric |
| Calculate metric using overlapping amplified/deleted regions | calculateOverlapMetric |
| Is an object of class 'CNVMetric' | is.CNVMetric |
| Plot metrics present in a 'CNVMetric' object | plotMetric |
| Print CNVMetric object | print.CNVMetric |
| Generate simulated samples with copy number profiles derived from a specific sample | processSim |
