Package: deltaCaptureC 1.21.0
Michael Shapiro
deltaCaptureC: This Package Discovers Meso-scale Chromatin Remodeling from 3C Data
This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred 'viewpoint' region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments.
Authors:
deltaCaptureC_1.21.0.tar.gz
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deltaCaptureC.pdf |deltaCaptureC.html✨
deltaCaptureC/json (API)
| # Install 'deltaCaptureC' in R: |
| install.packages('deltaCaptureC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- bigBinSize - Big bin size
- binnedDeltaPlot - Plot of Binned Delta Counts
- binnedDeltaSE - Binned difference of mean capture-C counts between EScells and Neurons
- binnedSummarizedExperiment - Binned Capture-C counts of EScells and Neurons
- deltaSE - Difference of mean capture-C counts between EScells and Neurons
- miniDeltaSE - Difference of mean capture-C counts between EScells and Neurons
- miniSE - Capture-C counts of EScells and Neurons
- miniSEDF - Capture-C counts of EScells and Neurons
- numPermutations - Number of permutations used in example permutation testing.
- pValue - P-value
- plotTitle - Title for delta capture-C plot
- regionOfInterest - Region of interest surrounding the viewpoint
- significanceType - Type for testing significance
- significantRegions - Regions of significant remodeling in example data
- significantRegionsPlot - A plot of the significant regions in the sample data.
- smallBinSize - Small Bin Size
- smallBins - Small Bins
- smallSetOfSmallBins - Small Bins
- smallerDeltaSE - A subset of miniDeltaSE.
- viewpointRegion - Region surrounding the viewpoint
- weightsExampleBins - Weights example bins
- weightsExampleGr - Weights example
On BioConductor:deltaCaptureC-1.21.0(bioc 3.21)deltaCaptureC-1.20.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
biologicalquestionstatisticalmethod
Last updated 23 days agofrom:10a66b36c0. Checks:OK: 1 WARNING: 4 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 03 2024 |
| R-4.5-win | WARNING | Nov 03 2024 |
| R-4.5-linux | WARNING | Nov 03 2024 |
| R-4.4-win | WARNING | Nov 03 2024 |
| R-4.4-mac | NOTE | Nov 03 2024 |
| R-4.3-win | WARNING | Nov 03 2024 |
| R-4.3-mac | NOTE | Nov 03 2024 |
Exports:binSummarizedExperimentdownshiftDFtoMatrixgeneratePermutationgetDeltaSEgetLopsidednessgetMeanNormalizedCountsSEgetNormalizedCountsSEgetOverlapWeightsgetPValueCutoffgetRunAndLopsidednessStatisticsgetRunStatisticsDistgetRunTotalsgetSignificantRegionsgetSizeFactorsDFgetSizeFactorsSEplotSignificantRegionsrebinToMultiple
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelclicodetoolscolorspacecpp11crayoncurlDelayedArrayDESeq2fansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcppRcppArmadillorlangS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbletictocUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
