Package: ribiosExpression 1.3.5

Jitao David Zhang

ribiosExpression: Data Structures and Utilities for Gene Expression Analysis

Provides data structures and utility functions for gene expression analysis. It includes the DesignContrast class for representing study designs and contrasts used in differential expression analysis, functions for importing and exporting expression data in GCT/CLS formats, tools for probeset summarization and filtering, and interfaces to limma-based differential gene expression workflows. The package works with Biobase ExpressionSet objects and integrates with the limma framework.

Authors:Jitao David Zhang [aut, cre]

ribiosExpression_1.3.5.tar.gz
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ribiosExpression_1.3.5.tgz(r-4.6-any)ribiosExpression_1.3.5.tgz(r-4.5-any)
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ribiosExpression_1.3.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ribiosExpression/json (API)

# Install 'ribiosExpression' in R:

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

Bug tracker:https://github.com/bedapub/ribiosexpression/issues

Datasets:

ribios.ExpressionSet - An ExpressionSet for case demonstrations
ribiosExpressionSet - RibiosExpressionSet: An example of ExpressionSet with artificial expression data

On CRAN:

geneexpression differentialexpression microarray dataimport visualization

4.18 score 2 packages 17 scripts 73 exports 69 dependencies

Last updated from:51b5fd3271. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	246
source / vignettes	OK	274
linux-release-x86_64	NOTE	215
macos-release-arm64	NOTE	202
macos-oldrel-arm64	NOTE	187
windows-devel	NOTE	184
windows-release	NOTE	181
windows-oldrel	NOTE	172
wasm-release	OK	124

Exports:annotate annotation annotation<-assayData assertFullRank avgReplicates contrastAnnotation contrastAnnotation<-contrastMatrix contrastMatrix<-contrastNames contrastSampleIndices dataFrameTwoVecs design2group DesignContrast designMatrix designMatrix<-designVariables dispGroups eSetToLongTable exprs exprs<-exprsToLong fData fData<-featureData featureNames featureNames<-fixDesignMatrixColnames fixEmptyColumnName formatGmt groups grp2gmt grpFiles2gmt keepMaxStatProbe limmaDgeTable limmaTopTable2dgeTable matrixToLongTable medianReplicates mergeEset nContrast parseContrastStr parseDesignContrast parseDesignContrastFile parseDesignContrastStr pData pData<-phenoData poolReplicates readAnnotationFile readEset readExprsMatrix readFeatureAnnotationFile readFKtable readGct readGctCls readSampleAnnotationFile reannotate removeAllZeroVar removeColRank sampleNames show sniffFeatureType splitPCA summarizeProbesets summarizeSamples truncateDgeTable writeCls writeEset writeGct writeGctCls writeSampleGroups writeVarMetadata

Dependencies:askpass Biobase BiocGenerics circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon digest doParallel dplyr farver foreach generics GetoptLong ggplot2 GlobalOptions glue gridExtra gtable IRanges isoband iterators jsonlite labeling lattice lifecycle limma magrittr Matrix matrixStats mime mongolite openssl openxlsx pillar pkgconfig png purrr R6 RColorBrewer Rcpp ribiosAnnotation ribiosArg ribiosIO ribiosPlot ribiosUtils rjson rlang S4Vectors S7 scales shape statmod stringi stringr sys tibble tidyr tidyselect utf8 vctrs viridisLite withr zip

Introduction to ribiosExpression

Rendered fromribiosExpression.Rmdusingknitr::rmarkdown

Last update: 2026-02-13
Started: 2026-02-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annotate eSet or probesets	annotate
Assert whether a matrix is of full rank numerically	assertFullRank
Extract the contrast annotation data.frame from an object	contrastAnnotation contrastAnnotation,DesignContrast-method contrastAnnotation<-,DesignContrast-method
Assign contrast annotation to an object	contrastAnnotation<-
Extract the contrast matrix from an object	contrastMatrix contrastMatrix,DesignContrast-method contrastMatrix,MArrayLM-method contrastMatrix<-,DesignContrast-method
Assign contrast matrix to an object	contrastMatrix<-
Extract contrastNames from an object	contrastNames contrastNames,DesignContrast-method contrastNames,MArrayLM-method
Return indices of samples involved in the given contrast of two or more coefficients	contrastSampleIndices contrastSampleIndices,DesignContrast,character-method contrastSampleIndices,DesignContrast,numeric-method
Build a data.frame from two vectors of potential different lengths	dataFrameTwoVecs
Infer groups from a design matrix	design2group
Contrast a DesignContrast object	DesignContrast
Study design and contrast information	DesignContrast-class show,DesignContrast-method
Extract the design matrix from an object	designMatrix designMatrix,DesignContrast-method designMatrix,MArrayLM-method designMatrix<-,DesignContrast-method
Assign design matrix to an object	designMatrix<-
Extract design variable names from an object	designVariables designVariables,DesignContrast-method
Extract displayed group labels from an object	dispGroups dispGroups,DesignContrast-method
Transform eSet to long data.frame	eSetToLongTable
Transform an expression matrix to long table	exprsToLong exprsToLong,eSet-method exprsToLong,matrix-method exprsToLong-eSet-method exprsToLong-matrix-method
Fix design matrix colnames so that they are legal variable names	fixDesignMatrixColnames
Detect if any column has an empty string as name and fix	fixEmptyColumnName
Make strings in the GMT format	formatGmt formatGmt,character,character,character-method formatGmt,character,character,list-method formatGmt,character,missing,character-method formatGmt,character,missing,list-method
Extract sample groups from an object	groups groups,DesignContrast-method
Convert GRP files into GMT-formatted strings	grp2gmt grpFiles2gmt
Test whether the input design matrix is consistent with the sample names	isInputDesignConsistent
Filter multiple probesets matching to the same gene by keeping the one with the maximum statistic (by default the variance).	keepMaxStatProbe
Return dgeTable from a marrayLM object	limmaDgeTable
Transform limma::topTable results to a DGEtable	limmaTopTable2dgeTable
Transform a matrix to long table	matrixToLongTable
Merge two eSets by column binding	mergeEset
Extract the number of contrasts from an object	nContrast nContrast,DesignContrast-method
Parse contrast from strings	parseContrastStr
Parse study design and asked questions encoded in design and contrast matrices or in one-way ANOVA designs	parseDesignContrast
Parse design and contrast from files	parseDesignContrastFile
Parse design and contrast from strings	parseDesignContrastStr
Plot a DesignContrast object with two heatmaps	plot.DesignContrast
Read in an annotation file in the tsv-format, with or without row names	readAnnotationFile
Read eSet object from plain files	readEset
Read an expression matrix into an ExpressionSet object	readExprsMatrix
Read in feature annotation file in the tsv-format, with or without row names	readFeatureAnnotationFile
Read table with Foreign Keys	readFKtable
Import ExpressionSet into gct/cls files the C version, about 5x faster than the R implementation for the ALL dataset	readGct readGctCls read_cls
Read in sample annotation file in the tsv-format, with or without row names	readSampleAnnotationFile
Transform an eSet object of Bioc-annotation into of GTI-annotation	reannotate reannotate,eSet,logical-method reannotate,eSet,missing-method
Remove all-zero variables from design matrix and the corresponding contrast matrix	removeAllZeroVar removeAllZeroVar.DesignContrast removeAllZeroVar.matrix
Return rank of the matrix and the ranks of resulting matrices when each column is removed	removeColRank
An ExpressionSet for case demonstrations	ribios.ExpressionSet
ribiosExpressionSet: An example of ExpressionSet with artificial expression data	ribiosExpressionSet
Perform row-wise scaling to an ExpressionSet object	rowscale.ExpressionSet
Sniff the feature type of an object that implements the featureNames method	sniffFeatureType
Split an eSet object and run PCA on each split, return PCA scores as one data.frame	splitPCA
Summarize probesets belonging to the same gene	summarizeProbesets
Summarize samples by applying the function to sample subsets	avgReplicates medianReplicates poolReplicates summarizeSamples
Truncate dgeTable into tables of positively and negatively differentially expressed genes according to the pre-defined criteria	truncateDgeTable
Export ExpressionSet as Gct/Cls files	eset2cls eset2gct writeCls writeGctCls
Export an ExpressionSet object as tab-delimited (or gct) files	writeEset
Export matrix or eSet that can be coerced as one into gct/cls files	writeGct writeGct,eSet,ANY,ANY,ANY-method writeGct,eSet-method writeGct,matrix,ANY,ANY,ANY-method writeGct,matrix-method
Write sample groups and group levels into plain text files	writeSampleGroups
writexlxs: write AnnotatedDataFrame to a xlsx file	writeVarMetadata writeVarMetadata.default