Package: Chicago 1.35.0
Mikhail Spivakov
Chicago: CHiCAGO: Capture Hi-C Analysis of Genomic Organization
A pipeline for analysing Capture Hi-C data.
Authors:
Chicago_1.35.0.tar.gz
Chicago_1.35.0.zip(r-4.5)Chicago_1.35.0.zip(r-4.4)Chicago_1.35.0.zip(r-4.3)
Chicago_1.35.0.tgz(r-4.4-any)Chicago_1.35.0.tgz(r-4.3-any)
Chicago_1.35.0.tar.gz(r-4.5-noble)Chicago_1.35.0.tar.gz(r-4.4-noble)
Chicago_1.35.0.tgz(r-4.4-emscripten)Chicago_1.35.0.tgz(r-4.3-emscripten)
Chicago.pdf |Chicago.html✨
Chicago/json (API)
NEWS
| # Install 'Chicago' in R: |
| install.packages('Chicago', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- cdUnitTest - ChicagoData object for unit testing
On BioConductor:Chicago-1.35.0(bioc 3.21)Chicago-1.34.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
epigeneticshicsequencingsoftware
Last updated 2 months agofrom:eb0001cef9. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | OK | Nov 29 2024 |
| R-4.4-mac | OK | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:chicagoDatachicagoPipelinecopyCDdefaultSettingsestimateBrownianComponentestimateBrownianNoiseestimateDistFunestimateTechnicalNoiseexportResultsexportToGIgetPvalsgetScoresgetSkOnlyintDataintData<-mergeSamplesmodifySettingsnormaliseBaitsnormaliseOtherEndsoverlapFragWithFeaturesparamsparams<-peakEnrichment4FeaturesplotBaitsplotDistFunreadAndMergereadSamplesetExperimentsettings
Dependencies:backportsbase64encbslibcachemcheckmatecliclustercolorspacedata.tableDelaportedigestevaluatefansifarverfastmapfontawesomeforeignFormulafsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetpillarpkgconfigR6rappdirsRColorBrewerrlangrmarkdownrpartrstudioapisassscalesstringistringrtibbletinytexutf8vctrsviridisviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CHiCAGO: Capture Hi-C Analysis of Genomic Organization | Chicago-package Chicago |
| ChicagoData object for unit testing | cdUnitTest |
| The 'chicagoData' class. | chicagoData intData intData,chicagoData-method intData<- intData<-,chicagoData-method params params,chicagoData-method params<- params<-,chicagoData-method settings settings,chicagoData-method |
| CHiCAGO pipeline function | chicagoPipeline |
| Copy chicagoData object | copyCD |
| Default CHiCAGO settings | defaultSettings |
| Estimate Brownian background component. | estimateBrownianComponent estimateBrownianNoise |
| Estimate the Distance Function | estimateDistFun |
| Estimate Technical Noise | estimateTechnicalNoise |
| Export Results | exportResults exportToGI |
| Get P-values | getPvals |
| Get CHiCAGO scores. | getScores |
| Get S_k factors from multiple replicates | getSkOnly |
| Merge samples together. | mergeSamples |
| Modify Settings | modifySettings |
| Normalise Baits | normaliseBaits |
| Normalise Other Ends | normaliseOtherEnds |
| Overlap Other-Ends with Features | overlapFragWithFeatures |
| Enrichment for Features | peakEnrichment4Features |
| Plot Baits | plotBaits |
| Plot the Distance Function | plotDistFun |
| Read And Merge | readAndMerge |
| Read Sample | readSample |
| Set Experiment | setExperiment |