Introduction | Workflow | Setup | Before you run PostChicago: | Run CHiCAGO | Read in the datasets | Basic statistics | Visualisation | Lineplots | Annotation of Line plots with intervals: | Creating Genome Browser tracks: | Data integration | Create interactions table | Visualize significant interactions using Lineplots | Quantification | Quantification within intervals of interest | Making oneGeneOnePeak tables | Matrices surrounding intervals of interest | Plotting aggregate profiles of interactions | Quantify reads in epigenetic peak interactions directly | Data integration to interaction peaks | Direct quantification within interaction peaks | Session Info | References
Package: PostChicago 0.99.2
Angelika Feldmann
PostChicago: PostChicago - visualization and integration of Capture-(Hi)C data
PostCHiCAGO (stylized from here as PostChicago) is a toolbox for visualising and assessing the output from the CHiCAGO pipeline (SOURCE). The plots created by PostChicago show reads or CHiCAGO scores over different regions. PostChicago can integrate different experiments with other types of datasets and compare separate conditions.
Authors:
PostChicago_0.99.2.tar.gz
PostChicago_0.99.2.zip(r-4.7)PostChicago_0.99.2.zip(r-4.6)PostChicago_0.99.2.zip(r-4.5)
PostChicago_0.99.2.tgz(r-4.6-any)PostChicago_0.99.2.tgz(r-4.5-any)
PostChicago_0.99.2.tar.gz(r-4.7-any)PostChicago_0.99.2.tar.gz(r-4.6-any)
PostChicago_0.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
PostChicago/json (API)
| # Install 'PostChicago' in R: |
| install.packages('PostChicago', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/feldmannlabdkfz/postchicago/issues
On BioConductor:PostChicago-0.99.2(bioc 3.24)
softwaregeneregulationepigeneticsvisualization
Last updated from:9927510d79. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 206 | ||
| linux-devel-x86_64 | OK | 381 | ||
| source / vignettes | OK | 317 | ||
| linux-release-x86_64 | OK | 440 | ||
| macos-release-arm64 | OK | 313 | ||
| macos-oldrel-arm64 | OK | 187 | ||
| windows-devel | OK | 299 | ||
| windows-release | OK | 289 | ||
| windows-oldrel | OK | 312 | ||
| wasm-release | OK | 164 |
Exports:aggregatePeaksaggregatePeaks_regionsannotateIntsbaitmap2baited_genesboxplotsCapCgetMatrixloadCdListloadGrlmakeBedGraphsmakeIntsTablemakeOneGeneOnePeakmakeQCplotsplotAggregatePeaksplotInteractionsplotSigIntsStatsquantifyWithinPeaksrmap2rmapgrrunChicagoForPostChicago
Dependencies:abindaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbslibcachemcheckmateChicagocigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelaporteDelayedArraydigestdplyrevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpatchworkpheatmappillarpkgconfigpurrrR6rappdirsRColorBrewerRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregate Interactions to Interaction Peaks | aggregatePeaks |
| Aggregate Interactions to Interaction Peaks by Distance in bp | aggregatePeaks_regions |
| Annotate Interactions | annotateInts |
| Convert baitmap to baited_genes | baitmap2baited_genes |
| Boxplots of summarized interactions data. | boxplotsCapC |
| Create Interaction Matrices | getMatrix |
| Loads List with Interaction Tables | loadCdList |
| Load Intervals into a GenomicRangesList | loadGrl |
| Create Bedgraphs From ChicagoData | makeBedGraphs |
| Create Interactions Table | makeIntsTable |
| Make one-Gene-one-Peak Interaction Tables. | makeOneGeneOnePeak |
| Quality Control Plots | makeQCplots |
| Plot Aggregate Interaction Profiles | plotAggregatePeaks |
| Plot Lineplots of Interactions | plotInteractions |
| Plot Interaction Statistics | plotSigIntsStats |
| Quantification of Reads and Scores within oneGeneOnePeak or AggregatedPeak Interactions. | quantifyWithinPeaks |
| Convert .rmap to the GenomicRanges object 'rmapgr' | rmap2rmapgr |
| Run Chicago and save ChicagoData objects. | runChicagoForPostChicago |
