Package: AgiMicroRna 2.57.0

Pedro Lopez-Romero

AgiMicroRna: Processing and Differential Expression Analysis of Agilent microRNA chips

Processing and Analysis of Agilent microRNA data

Authors:Pedro Lopez-Romero <[email protected]>

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AgiMicroRna.pdf |AgiMicroRna.html✨
AgiMicroRna/json (API)

# Install 'AgiMicroRna' in R:

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

Datasets:

dd.micro - Data example
ddPROC - Processed miRNA data
targets.micro - Example of target file

On BioConductor:AgiMicroRna-2.55.0(bioc 3.20)AgiMicroRna-2.54.0(bioc 3.19)

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

microarray agilentchip onechannel preprocessing differentialexpression

3.30 score 9 scripts 452 downloads 23 exports 189 dependencies

Last updated 2 months agofrom:0da1667d0b. Checks:OK: 1 ERROR: 1 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	WARNING	Oct 30 2024
R-4.5-linux	ERROR	Oct 30 2024
R-4.4-win	WARNING	Oct 30 2024
R-4.4-mac	WARNING	Oct 30 2024
R-4.3-win	WARNING	Oct 30 2024
R-4.3-mac	WARNING	Oct 30 2024

Exports:basicLimma boxplotMicroRna cvArray esetMicroRna filterMicroRna getDecideTests HeatMapMicroRna hierclusMicroRna mvaBASIC mvaMicroRna PCAplotMicroRna plotDensityMicroRna pvalHistogram qcPlots readMicroRnaAFE readTargets RleMicroRna rmaMicroRna show significantMicroRna tgsMicroRna tgsNormalization writeEset

Dependencies:abind affy affycoretools affyio annotate AnnotationDbi AnnotationFilter AnnotationForge askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem Category caTools checkmate cli 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 highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 hwriter IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling 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 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 UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 xtable XVector yaml zlibbioc

AgiMicroRna

Rendered fromAgiMicroRna.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Linear models Using limma	basicLimma
Boxplot	boxplotMicroRna
Coefficient of variation of replicated probes within array	cvArray
data example (uRNAList)	dd.micro
Processed miRNA data (uRNAList)	ddPROC
Retrieve the Dimensions of an uRNAList Object	dim.uRNAList length.uRNAList
Retrieve the Dimension Names of an uRNAList Object	dimnames.uRNAList dimnames<-.uRNAList
ExpressionSet object from a uRNAList	esetMicroRna
Filtering Genes	filterMicroRna
Differential expression analysis an multiplicity of the tests	getDecideTests
HeatMap	HeatMapMicroRna
Hierarchical clustering	hierclusMicroRna
MVA plot	mvaBASIC
MA plot	mvaMicroRna
PCA plot	PCAplotMicroRna
Density Plots of Intensity Signals	plotDensityMicroRna
Histogram of the p values	pvalHistogram
Plots for Quality Assessment	qcPlots
Read Agilent Feature Extraction txt data files	readMicroRnaAFE
read the target file	readTargets
Relative Log Expression	RleMicroRna
Getting the Total Gene Signal by RMA algorithm	rmaMicroRna
Summarize Differential Expression Results	significantMicroRna
Summaries of Microarray Data Objects	summary.uRNAList
Example of target file	targets.micro
Getting the Total Gene Signal	tgsMicroRna
Normalization Between Arrays	tgsNormalization
uRNAList - class	show,uRNAList-method uRNAList-class
Writes the expression data matrix of an ExpressionSet object in a txt file	writeEset