Package: affycoretools 1.77.0

James W. MacDonald

affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.

Authors:James W. MacDonald

affycoretools_1.77.0.tar.gz
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affycoretools.pdf |affycoretools.html✨
affycoretools/json (API)
NEWS

# Install 'affycoretools' in R:

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

On BioConductor:affycoretools-1.77.0(bioc 3.20)affycoretools-1.76.0(bioc 3.19)

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

bioconductor-package

25 exports 1.16 score 196 dependencies 1 dependents 36 mentions

Last updated 2 months agofrom:ee5d3dfd90

Exports:affyLinks affystart annotateEset doGlimma ensemblLinks entrezLinks getMainProbes goLinks makeGoTable makeHmap makeImages makeVenn maplot mirna2mrna nuccoreLinks outputRomer plotDeg plotHist plotPCA runRomer vennCounts2 vennInLine vennPage vennSelect2 writeFit

Dependencies:abind affy affyio annotate AnnotationDbi AnnotationFilter AnnotationForge askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob broom broom.helpers BSgenome bslib cachem Category caTools checkmate cli clipr cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray DESeq2 dichromat digest dplyr edgeR ensembldb evaluate fansi farver fastmap ff filelock fontawesome forcats foreach foreign formatR Formula fs futile.logger futile.options gcrma genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GGally ggbio ggplot2 ggstats Glimma glue GO.db GOstats gplots graph gridExtra GSEABase gtable gtools haven highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 hwriter IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling labelled lambda.r lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet oligoClasses openssl OrganismDbi patchwork PFAM.db pillar pkgconfig plogr plyr png preprocessCore prettyunits progress ProtGenerics purrr R.methodsS3 R.oo R.utils R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RCurl readr ReportingTools reshape2 restfulr Rgraphviz Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex txdbmaker tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc

Creating annotated output with \Biocpkg{affycoretools} and ReportingTools

James W. MacDonald

Rendered fromRefactoredAffycoretools.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2018-02-02
Started: 2017-11-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Make repetitive analyses of microarray and RNA-Seq data simpler with affycoretools.	affycoretools
Pre-processing for Affymetrix Data	affystart
Method to annotate ExpressionSets automatically	annotateEset annotateEset,ExpressionSet,AffyExonPDInfo-method annotateEset,ExpressionSet,AffyExpressionPDInfo-method annotateEset,ExpressionSet,AffyGenePDInfo-method annotateEset,ExpressionSet,AffyHTAPDInfo-method annotateEset,ExpressionSet,character-method annotateEset,ExpressionSet,ChipDb-method annotateEset,ExpressionSet,data.frame-method
A function to create an annotated HTML table for all genes in a significant gene set as well as a heatmap of these data.	dataAndHeatmapPage
A function to generate MA-plots from Glimma, for all contrasts.	doGlimma
Add links to data when using ReportingTools	affyLinks ensemblLinks entrezLinks goLinks nuccoreLinks
Fix data.frame header for use with ReportingTools	fixHeaderAndGo
A function to create an HTML page for each gene set, as well as the HTML pages for each significant gene set.	geneSetPage
Remove control probesets from ST arrays	getMainProbes
A function to create a simple heatmap and key.	gsHeatmap
Make Gene table from GO analysis results	makeGoGeneTable
Create HTML tables for Gene Ontology (GO) analyses	makeGoTable
A function to create a heatmap-like object or matrix of correlations between miRNA and mRNA data.	makeHmap
Add dotplot images	makeImages
High-level function for making Venn diagrams and outputting the results from the diagrams in HTML and CSV files.	makeVenn makeVenn,DGEGLM-method makeVenn,MArrayLM-method
A Function to make MA plots from all arrays.	maplot
A function to map miRNA to mRNA.	mirna2mrna
A function to create HTML output from the results of running romer on a set of contrasts.	outputRomer outputRomer,DGEList,DGEGLM-method outputRomer,EList,MArrayLM-method outputRomer,ExpressionSet,MArrayLM-method
Functions to Plot Density and RNA Degradation Plots	plotDeg plotHist
A Function to Make a PCA Plot from an ExpressionSet or matrix	plotPCA plotPCA,ExpressionSet-method plotPCA,matrix-method
A function to run the romer function on a set of contrasts.	runRomer runRomer,DGEList-method runRomer,EList-method runRomer,ExpressionSet-method
4-way Venn Diagrams	venn4Way
Compute Counts for Venn Diagram	vennCounts2
Generate Venn diagrams with links for Rmarkdown documents	vennInLine
High-level function for making Venn diagrams with clickable links to HTML pages with the underlying genes.	vennPage
Select and Output Genelists Based on Venn Diagrams	vennSelect2
Function to output annotated fit data from limma	writeFit