Package: NanoStringNCTools 1.15.0

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]

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NanoStringNCTools.pdf |NanoStringNCTools.html✨
NanoStringNCTools/json (API)
NEWS

# Install 'NanoStringNCTools' in R:

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

On BioConductor:NanoStringNCTools-1.13.0(bioc 3.20)NanoStringNCTools-1.12.0(bioc 3.19)

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

6.44 score 4 packages 77 scripts 618 downloads 68 exports 79 dependencies

Last updated 20 days agofrom:daac9af5da. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

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:askpass base64enc beeswarm Biobase BiocGenerics Biostrings bslib cachem cli colorspace cpp11 crayon curl digest evaluate fansi farver fastmap fontawesome fs GenomeInfoDb GenomeInfoDbData ggbeeswarm ggiraph ggplot2 ggthemes glue gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite knitr labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pheatmap pillar pkgconfig purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S4Vectors sass scales stringi stringr sys systemfonts tibble tinytex UCSC.utils utf8 uuid vctrs vipor viridisLite withr xfun XVector yaml zlibbioc

Introduction to the NanoStringRCCSet Class

David Henderson, Patrick Aboyoun, Nicole Ortogero, Zhi Yang, Jason Reeves, Kara Gorman, Rona Vitancol, Thomas Smith, Yuqi Ren

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Oct 30 2024.

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