Introduction | Workflow | Input files required | Example workflow | Output plots | Interpreting the plots | Output files | ibed format (ends with ...ibed): | seqmonk format (ends with ...seqmonk.txt): | washU_text format (ends with ...washU_text.txt): | Visualising interactions | Peak enrichment for features | Further downstream analysis | The chicagoData object
Package: Chicago 1.41.0
Mikhail Spivakov
Chicago: CHiCAGO: Capture Hi-C Analysis of Genomic Organization
A pipeline for analysing Capture Hi-C data.
Authors:
Chicago_1.41.0.tar.gz
Chicago_1.41.0.zip(r-4.7)Chicago_1.41.0.zip(r-4.6)Chicago_1.41.0.zip(r-4.5)
Chicago_1.41.0.tgz(r-4.6-any)Chicago_1.41.0.tgz(r-4.5-any)
Chicago_1.41.0.tar.gz(r-4.7-any)Chicago_1.41.0.tar.gz(r-4.6-any)
Chicago_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Chicago/json (API)
| # Install 'Chicago' in R: |
| install.packages('Chicago', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- cdUnitTest - ChicagoData object for unit testing
On BioConductor:Chicago-1.41.0(bioc 3.24)Chicago-1.40.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
epigeneticshicsequencingsoftware
Last updated from:2e8e18aae4. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 228 | ||
| linux-devel-x86_64 | NOTE | 363 | ||
| source / vignettes | OK | 350 | ||
| linux-release-x86_64 | NOTE | 327 | ||
| macos-release-arm64 | NOTE | 137 | ||
| macos-oldrel-arm64 | NOTE | 134 | ||
| windows-devel | NOTE | 232 | ||
| windows-release | NOTE | 219 | ||
| windows-oldrel | NOTE | 199 | ||
| wasm-release | OK | 214 |
Exports:chicagoDatachicagoPipelinecopyCDdefaultSettingsestimateBrownianComponentestimateBrownianNoiseestimateDistFunestimateTechnicalNoiseexportResultsexportToGIgetPvalsgetScoresgetSkOnlyintDataintData<-mergeSamplesmodifySettingsnormaliseBaitsnormaliseOtherEndsoverlapFragWithFeaturesparamsparams<-peakEnrichment4FeaturesplotBaitsplotDistFunreadAndMergereadSamplesetExperimentsettings
Dependencies:backportsbase64encbslibcachemcheckmatecliclustercolorspacecpp11data.tableDelaportedigestevaluatefarverfastmapfontawesomeforeignFormulafsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglifecyclemagrittrMASSmatrixStatsmemoisemimennetR6rappdirsRColorBrewerrlangrmarkdownrpartrstudioapiS7sassscalesstringistringrtinytexvctrsviridisLitewithrxfunyaml
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 |