Package: soGGi 1.37.0
Tom Carroll
soGGi: Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals
The soGGi package provides a toolset to create genomic interval aggregate/summary plots of signal or motif occurence from BAM and bigWig files as well as PWM, rlelist, GRanges and GAlignments Bioconductor objects. soGGi allows for normalisation, transformation and arithmetic operation on and between summary plot objects as well as grouping and subsetting of plots by GRanges objects and user supplied metadata. Plots are created using the GGplot2 libary to allow user defined manipulation of the returned plot object. Coupled together, soGGi features a broad set of methods to visualise genomics data in the context of groups of genomic intervals such as genes, superenhancers and transcription factor binding events.
Authors:
soGGi_1.37.0.tar.gz
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soGGi.pdf |soGGi.html✨
soGGi/json (API)
NEWS
| # Install 'soGGi' in R: |
| install.packages('soGGi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- chipExampleBig - Example ChIPprofiles
- ik_Example - Example Ikaros peaksets
- ik_Profiles - Example Ikaros signal over peaksets
- pwmCov - Example motif coverage
- singleGRange - A single GRange
On BioConductor:soGGi-1.37.0(bioc 3.20)soGGi-1.36.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 months agofrom:f0e0c410e6. Checks:ERROR: 2 NOTE: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Sep 30 2024 |
| R-4.5-win | NOTE | Sep 30 2024 |
| R-4.5-linux | ERROR | Sep 30 2024 |
| R-4.4-win | NOTE | Sep 30 2024 |
| R-4.4-mac | NOTE | Sep 30 2024 |
| R-4.3-win | NOTE | Sep 30 2024 |
| R-4.3-mac | NOTE | Sep 30 2024 |
Exports:cbindfindconsensusRegionsgroupByOverlapsmakeMotifScoreRlemeannormalisenormalise.ChIPprofilenormaliseQuantilesnormaliseQuantiles.ChIPprofileOpsorientByplotRegionpwmToCoveragerbindregionPlotsummitPipeline
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopschipseqclicodetoolscolorspacecpp11crayoncurlDelayedArraydeldirfansifarverformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrhwriterinterpIRangesisobandjpegjsonlitelabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrpngpreprocessCorepwalignR6RColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalesShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc
soggi
Rendered fromsoggi.Rnwusingknitr::knitron Sep 30 2024.Last update: 2015-05-12
Started: 2015-04-06
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Join, subset and manipulate ChIPprofile objects | $,ChIPprofile-method c,ChIPprofile-method cbind,ChIPprofile-method rbind,ChIPprofile-method [[,ChIPprofile,ANY,missing-method |
| Example ChIPprofiles | chipExampleBig |
| The soggi function and ChIPprofile object. | ChIPprofile ChIPprofile-ChIPprofile ChIPprofile-class regionPlot soggi |
| Plot coverage of points or regions. | findconsensusRegions summitPipeline |
| Create GRangeslist from all combinations of GRanges | groupByOverlaps |
| Example Ikaros peaksets | ik_Example |
| Example Ikaros signal over peaksets | ik_Profiles |
| Normalise ChIPprofiles | normalise normalise,ChIPprofile,character,numeric-method normalise,ChIPprofile-method normalise.ChIPprofile |
| Normalise quantile | normaliseQuantiles normaliseQuantiles,ChIPprofile-method normaliseQuantiles.ChIPprofile |
| Arithmetic operations | log,ChIPprofile-method log2,ChIPprofile-method mean,ChIPprofile-method Ops,ChIPprofile,ChIPprofile-method Ops,ChIPprofile,numeric-method Ops,numeric,ChIPprofile-method |
| Set strand by overlapping or nearest anchor GRanges | orientBy |
| Plot regions | plotRegion plotRegion,ChIPprofile-method plotRegion.ChIPprofile |
| Example motif coverage | pwmCov |
| PWM hits and motif scores as an RLElist | makeMotifScoreRle pwmToCoverage |
| A single GRange | singleGRange |
