Package: epigenomix 1.47.0
Hans-Ulrich Klein
epigenomix: Epigenetic and gene transcription data normalization and integration with mixture models
A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.
Authors:
epigenomix_1.47.0.tar.gz
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epigenomix_1.47.0.tgz(r-4.4-any)epigenomix_1.47.0.tgz(r-4.3-any)
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epigenomix.pdf |epigenomix.html✨
epigenomix/json (API)
| # Install 'epigenomix' in R: |
| install.packages('epigenomix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- eSet - Example gene expression data set.
- fpkm - Example RNA-seq data set.
- mappedReads - Mapped reads obtained from a anti-histone ChIP-seq experiment.
- transToTSS - A data frame with Ensemble transcript IDs and transcriptional start sites.
On BioConductor:epigenomix-1.45.0(bioc 3.20)epigenomix-1.44.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
chipseqgeneexpressiondifferentialexpressionclassification
Last updated 26 days agofrom:6b8078f870. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:acceptanceRateas.data.framebayesMixModelcalculateCrossCorrelationchainsChIPseqSetchipValschipVals<-classificationcomponentsconvergencecpmgetAlignmentQualityintegrateDatalistClassificationMethodsmatchProbeToPromotermlMixModelmmDatanormalizenormalizeChIPplotChainsplotClassificationplotComponentsshowsummarizeReadssummaryweights
Dependencies:abindAnnotationDbiaskpassbase64beadarrayBeadDataPackRBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobcachemclicodacodetoolscolorspacecpp11crayoncurlDBIDelayedArrayfansifarverfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehexbinhttrilluminaioIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmcmcMCMCpackmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngquantregR6RColorBrewerRcppreshape2RhtslibrlangRsamtoolsRSQLiteS4ArraysS4VectorsscalessnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Fits a Bayesian mixture model using Markov Chain Monte Carlo (MCMC) methods | bayesMixModel bayesMixModel,numeric-method |
| Calculate the cross correlation for a given GRanges object. | calculateCrossCorrelation calculateCrossCorrelation,GRanges-method |
| Class '"ChIPseqSet"' | ChIPseqSet ChIPseqSet,matrix,GRanges-method ChIPseqSet,matrix,GRangesList-method ChIPseqSet-class chipVals chipVals,ChIPseqSet-method chipVals<- chipVals<-,ChIPseqSet,matrix-method cpm cpm,ChIPseqSet-method |
| Example gene expression data set. | eSet |
| Example RNA-seq data set. | fpkm |
| Calculation of basic alignments statistics | getAlignmentQuality getAlignmentQuality,character-method |
| Calculates a normalized correlation score from ChIP-seq and microarray gene expression data. | integrateData integrateData,ExpressionSet,ChIPseqSet,character,character-method integrateData,ExpressionSet,ChIPseqSet,character,missing-method integrateData,ExpressionSetIllumina,ChIPseqSet,character,character-method integrateData,ExpressionSetIllumina,ChIPseqSet,character,missing-method |
| Mapped reads obtained from a anti-histone ChIP-seq experiment. | mappedReads |
| A function assigning promoter regions to given probe IDs. | matchProbeToPromoter matchProbeToPromoter,list,data.frame-method |
| Class '"MixModel"' | as.data.frame,MixModel-method classification classification,MixModel,character-method classification,MixModel,missing-method components components,MixModel-method dim,MixModel-method length,MixModel-method listClassificationMethods listClassificationMethods,MixModel-method MixModel-class mmData mmData,MixModel-method show,MixModel-method summary,MixModel-method summary,MixModelBayes-method weights,MixModel-method |
| Class '"MixModelBayes"' | acceptanceRate acceptanceRate,MixModelBayes-method chains chains,MixModelBayes-method MixModelBayes-class |
| Class '"MixModelML"' | convergence convergence,MixModelML-method MixModelML-class |
| Class '"MixtureComponent"' | MixtureComponent-class show,MixtureComponent-method |
| Fits a mixture model using the maximum likelihood principle. | mlMixModel mlMixModel,numeric-method |
| Normalization of ChIP-seq and other count data | normalize normalize,ChIPseqSet-method normalize,ExpressionSet-method |
| Normalization of ChIP-seq count data. (deprecated) | normalizeChIP normalizeChIP,ChIPseqSet,character-method |
| Produces trace plots for a Bayesian mixture model | plotChains plotChains,MixModelBayes-method |
| Plot classification obtained from a mixture model. | plotClassification plotClassification,MixModel-method |
| Plots the mixture density together with the densities of all single components. | plotComponents plotComponents,MixModel-method |
| Count reads lying within given regions. | summarizeReads summarizeReads,GRangesList,GRanges,character-method summarizeReads,GRangesList,GRanges,missing-method summarizeReads,GRangesList,GRangesList,character-method summarizeReads,GRangesList,GRangesList,missing-method |
| A data frame with Ensemble transcript IDs and transcriptional start sites. | transToTSS |