Package: epigenomix 1.53.0

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:Hans-Ulrich Klein, Martin Schaefer

epigenomix_1.53.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
epigenomix/json (API)

# Install 'epigenomix' in R:

install.packages('epigenomix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

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-1.53.0(bioc 3.24)epigenomix-1.52.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

chipseq geneexpression differentialexpression classification

3.30 score 1 scripts 1 mentions 27 exports 87 dependencies

Last updated from:924c8534c3. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	223
linux-devel-x86_64	NOTE	416
source / vignettes	OK	276
linux-release-x86_64	NOTE	443
macos-release-arm64	NOTE	210
macos-oldrel-arm64	NOTE	178
windows-devel	NOTE	315
windows-release	NOTE	345
windows-oldrel	NOTE	339
wasm-release	OK	161

Exports:acceptanceRate as.data.frame bayesMixModel calculateCrossCorrelation chains ChIPseqSet chipVals chipVals<-classification components convergence cpm getAlignmentQuality integrateData listClassificationMethods matchProbeToPromoter mlMixModel mmData normalize normalizeChIP plotChains plotClassification plotComponents show summarizeReads summary weights

Dependencies:abind AnnotationDbi askpass beadarray BeadDataPackR BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob cachem cli coda codetools cpp11 crayon curl DBI DelayedArray farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicRanges ggplot2 glue gtable hexbin httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mcmc MCMCpack memoise mime openssl pkgconfig plyr png quantreg R6 RColorBrewer Rcpp reshape2 Rhtslib rlang Rsamtools RSQLite S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys UCSC.utils vctrs viridisLite withr XVector

epigenomix package vignette

Introduction | Data preprocessing and normalization | ChIP-seq data normalization | Data integration | Classification by mixture models

Rendered fromepigenomix.Rnwusingutils::Sweave

Last update: 2017-04-09
Started: 2013-11-01

Citation

Development and contributors

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