Package: iCheck 1.37.0

Weiliang Qiu

iCheck: QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.

Authors:Weiliang Qiu [aut, cre], Brandon Guo [aut, ctb], Christopher Anderson [aut, ctb], Barbara Klanderman [aut, ctb], Vincent Carey [aut, ctb], Benjamin Raby [aut, ctb]

iCheck_1.37.0.tar.gz
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iCheck.pdf |iCheck.html✨
iCheck/json (API)
NEWS

# Install 'iCheck' in R:

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

On BioConductor:iCheck-1.37.0(bioc 3.21)iCheck-1.36.0(bioc 3.20)

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

geneexpression differentialexpression microarray preprocessing dnamethylation onechannel twochannel qualitycontrol

3.00 score 1 scripts 216 downloads 5 mentions 19 exports 179 dependencies

Last updated 2 months agofrom:3a391bfae6. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 30 2024
R-4.5-win	WARNING	Nov 30 2024
R-4.5-linux	WARNING	Nov 30 2024
R-4.4-win	WARNING	Nov 30 2024
R-4.4-mac	WARNING	Nov 30 2024
R-4.3-win	WARNING	Nov 30 2024
R-4.3-mac	WARNING	Nov 30 2024

Exports:boxPlots densityPlots genExprSet genSimData.BayesNormal getPCAFunc glmWrapper lkhrWrapper lmFitPaired lmFitWrapper LumiBatch2Table pca2DPlot pca3DPlot plotCurves plotQCCurves plotSamplep95p05 quantilePlot R2PlotFunc scatterPlots sortExpressionSet

Dependencies:abind affy affyio annotate AnnotationDbi askpass base64 base64enc beanplot BH Biobase BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob bslib bumphunter cachem caTools cli clipr codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doRNG dplyr evaluate fansi farver fastmap FDb.InfiniumMethylation.hg19 fontawesome foreach formatR fs futile.logger futile.options genefilter generics GeneSelectMMD GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gplots gtable gtools HDF5Array highr hms htmltools htmlwidgets httr httr2 illuminaio IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lifecycle limma lmtest locfit lumi magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi multtest munsell nleqslv nlme nor1mix openssl org.Hs.eg.db pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 randomForest rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape reshape2 restfulr rgl rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors sass scales scatterplot3d scrime selectr siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Draw parallel plots for top results in whole-genome-wide analysis	boxPlots
Draw estimated density plots for all arrays	densityPlots
Generate an ExpressionSet object	genExprSet
Generating simulated data set from conditional normal distributions	genSimData.BayesNormal
Get principal components of arrays	getPCAFunc
Perform glm test for all gene probes	glmWrapper
Perform glm test for all gene probes	lkhrWrapper
A wrapper function for the function 'lmFit' of the R Bioconductor package 'limma' for paired data	lmFitPaired
A wrapper function for the function 'lmFit' of the R Bioconductor package 'limma'	lmFitWrapper
Output slots (exprs, pData, fData) of an LumiBatch object into 3 text files	LumiBatch2Table
Scatter plot of first 2 principal components	pca2DPlot
Scatter plot of 3 specified principal components	pca3DPlot
Plot trajectories of probe profiles across arrays	plotCurves
Plot trajectories of specific QC probes (e.g., biotin, cy3_hyb, housekeeping gene probes, low stringency probes, etc.) across arrays	plotQCCurves
Plot trajectories of the ratio of 95th percentile to 5th percentile of sample probe profiles across arrays	plotSamplep95p05
Plot trajectories of quantiles across arrays	quantilePlot
Draw heatmap of square of correlations among arrays	R2PlotFunc
Draw scatter plots for top results in whole-genome-wide analysis	scatterPlots
Sort the order of samples for an ExpressionSet object	sortExpressionSet