NanoStringNCTools
This is the released version of NanoStringNCTools; for the devel version, see NanoStringNCTools.
NanoString nCounter Tools
Bioconductor version: Release (3.23)
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.
Author: Patrick Aboyoun [aut], Nicole Ortogero [aut], Maddy Griswold [cre], Zhi Yang [ctb]
Maintainer: Maddy Griswold <mgriswold at nanostring.com>
citation("NanoStringNCTools")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("NanoStringNCTools")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("NanoStringNCTools")| Introduction to the NanoStringRCCSet Class | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, DataImport, GeneExpression, ProprietaryPlatforms, Proteomics, RNASeq, Software, Transcription, Transcriptomics, mRNAMicroarray |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | MIT |
| Depends | R (>= 3.6), Biobase, S4Vectors, ggplot2 |
| Imports | BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes, grDevices, IRanges, methods, pheatmap, RColorBrewer, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf |
| Linking To | |
| Enhances | |
| Depends On Me | GeomxTools, GeoMxWorkflows |
| Imports Me | GeoDiff |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | NanoStringNCTools_1.20.0.tar.gz |
| Windows Binary (x86_64) | NanoStringNCTools_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | NanoStringNCTools_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | NanoStringNCTools_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/NanoStringNCTools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NanoStringNCTools |
| Bioc Package Browser | https://code.bioconductor.org/browse/NanoStringNCTools/ |
| Package Short Url | https://bioconductor.org/packages/NanoStringNCTools/ |
| Package Downloads Report | Download Stats |