Package: NanoStringNCTools 1.21.0

Maddy Griswold

NanoStringNCTools: NanoString nCounter Tools

Tools for NanoString Technologies nCounter Technology. Provides support for reading RCC files into an ExpressionSet derived object. Also includes methods for QC and normalizaztion of NanoString data.

Authors:Patrick Aboyoun [aut], Nicole Ortogero [aut], Maddy Griswold [cre], Zhi Yang [ctb]

NanoStringNCTools_1.21.0.tar.gz
NanoStringNCTools_1.21.0.zip(r-4.7)NanoStringNCTools_1.21.0.zip(r-4.6)NanoStringNCTools_1.21.0.zip(r-4.5)
NanoStringNCTools_1.21.0.tgz(r-4.6-any)NanoStringNCTools_1.21.0.tgz(r-4.5-any)
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NanoStringNCTools_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
NanoStringNCTools/json (API)

# Install 'NanoStringNCTools' in R:

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

On BioConductor:NanoStringNCTools-1.21.0(bioc 3.24)NanoStringNCTools-1.20.0(bioc 3.23)

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

geneexpression transcription cellbasedassays dataimport transcriptomics proteomics mrnamicroarray proprietaryplatforms rnaseq

6.79 score 4 packages 204 scripts 732 downloads 68 exports 71 dependencies

Last updated from:902fffc830. Checks:8 NOTE, 2 OK. Indexed: yes.

The latest version of this package failed to build. Look at thebuild logs for more information.

Target	Result	Time
bioc-checks	NOTE	312
linux-devel-x86_64	NOTE	420
source / vignettes	OK	380
linux-release-x86_64	NOTE	391
macos-release-arm64	NOTE	947
macos-oldrel-arm64	NOTE	161
windows-devel	NOTE	287
windows-release	NOTE	206
windows-oldrel	NOTE	176
wasm-release	OK	180

Exports:assayDataApply controlSubset design design<-dimLabels dimLabels<-endogenousSubset esBy fAbove fAtLeast fAtMost fBelow fCenter fIntCenter fIntScale fIntThresh fScale fThresh geom_beeswarm_interactive getSigFuncs groups groups<-housekeepingSubset log2t logt munge NanoStringRccSet negativeControlSubset nonControlSubset normalize positiveControlSubset readNanoStringRccSet readRccFile readRlfFile sAbove sAtLeast sAtMost sBelow sCenter sData setQCFlags setSignatureFuncs<-setSignatureGroups<-show signatureFuncs signatureGroups signatures signatures<-signatureScores signatureScoresApply SignatureSet signatureSubset sIntCenter sIntScale sIntThresh sScale sThresh subset summary svarLabels transform update_geom_params version version<-weights weights<-with writeNanoStringRccSet

Dependencies:base64enc beeswarm Biobase BiocGenerics Biostrings bslib cachem cli cpp11 crayon digest dplyr evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggbeeswarm ggiraph ggplot2 ggthemes glue gtable highr htmltools htmlwidgets IRanges isoband jquerylib jsonlite knitr labeling lifecycle magrittr MASS memoise mime pheatmap pillar pkgconfig purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S4Vectors S7 sass scales Seqinfo stringi stringr systemfonts tibble tidyselect tinytex utf8 vctrs vipor viridisLite withr xfun XVector yaml

Introduction to the NanoStringRCCSet Class

Rendered fromIntroduction.Rmdusingknitr::rmarkdown

Last update: 2024-04-11
Started: 2020-12-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Geometry for Interactive Bee Swarm Points	geom_beeswarm_interactive
Logarithm With Thresholding	log2t logt
Plot NanoStringRccSet Data	autoplot autoplot.NanoStringRccSet NanoStringRccSet-autoplot
Class to Contain NanoString Expression Level Assays	assayDataApply assayDataApply,NanoStringRccSet-method class:NanoStringRccSet coerce,ExpressionSet,NanoStringRccSet-method controlSubset controlSubset,NanoStringRccSet-method design,NanoStringRccSet-method design<-,NanoStringRccSet,ANY-method design<-,NanoStringRccSet,formula-method design<-,NanoStringRccSet,NULL-method dimLabels,NanoStringRccSet-method dimLabels<-,NanoStringRccSet,character-method endogenousSubset endogenousSubset,NanoStringRccSet-method esBy esBy,NanoStringRccSet-method ggplot.NanoStringRccSet housekeepingSubset housekeepingSubset,NanoStringRccSet-method munge munge,NanoStringRccSet-method NanoStringRccSet NanoStringRccSet,environment-method NanoStringRccSet,ExpressionSet-method NanoStringRccSet,matrix-method NanoStringRccSet,missing-method NanoStringRccSet,NanoStringRccSet-method NanoStringRccSet-class negativeControlSubset negativeControlSubset,NanoStringRccSet-method nonControlSubset nonControlSubset,NanoStringRccSet-method normalize,NanoStringRccSet-method positiveControlSubset positiveControlSubset,NanoStringRccSet-method sData sData,NanoStringRccSet-method setQCFlags,NanoStringRccSet-method setSignatureFuncs<- setSignatureFuncs<-,NanoStringRccSet,character-method setSignatureGroups<- setSignatureGroups<-,NanoStringRccSet,character-method setSignatureGroups<-,NanoStringRccSet,factor-method show,NanoStringRccSet-method signatureFuncs signatureFuncs,NanoStringRccSet-method signatureGroups signatureGroups,NanoStringRccSet-method signatures signatures,NanoStringRccSet-method signatures<- signatures<-,NanoStringRccSet,SignatureSet-method signatureScores signatureScores,NanoStringRccSet-method signatureScoresApply signatureScoresApply,NanoStringRccSet-method signatureSubset signatureSubset,NanoStringRccSet-method subset,NanoStringRccSet-method summary,NanoStringRccSet-method svarLabels svarLabels,NanoStringRccSet-method transform,NanoStringRccSet-method update_geom_params with,NanoStringRccSet-method [,NanoStringRccSet-method
Normalize RCCSet	normalize
Read 'NanoStringRccSet'	readNanoStringRccSet
Read RCC File	readRccFile
Read RLF File	readRlfFile
Set flags for QC of the assayData in a NanoStringRccSet.	setQCFlags
Class to Contain Signature Definitions	class:SignatureSet getSigFuncs getSigFuncs,SignatureSet-method groups groups,SignatureSet-method groups<- groups<-,SignatureSet,ANY-method groups<-,SignatureSet,factor-method groups<-,SignatureSet,NULL-method length,SignatureSet-method lengths,SignatureSet-method names,SignatureSet-method show,SignatureSet-method SignatureSet SignatureSet-class version version,SignatureSet-method version<- version<-,SignatureSet,ANY-method version<-,SignatureSet,character-method version<-,SignatureSet,NULL-method weights,SignatureSet-method weights<- weights<-,SignatureSet,ANY-method weights<-,SignatureSet,CompressedNumericList-method weights<-,SignatureSet,list-method weights<-,SignatureSet,NULL-method weights<-,SignatureSet,NumericList-method
Convenience Functions for Assay Data Element Sweep Operations	fAbove fAtLeast fAtMost fBelow fCenter fIntCenter fIntScale fIntThresh fScale fThresh sAbove sAtLeast sAtMost sBelow sCenter sIntCenter sIntScale sIntThresh sScale sThresh
Write NanoString Reporter Code Count (RCC) files	writeNanoStringRccSet