GeomxTools
This is the development version of GeomxTools; for the stable release version, see GeomxTools.
NanoString GeoMx Tools
Bioconductor version: Development (3.24)
Tools for NanoString Technologies GeoMx Technology. Package provides functions for reading in DCC and PKC files based on an ExpressionSet derived object. Normalization and QC functions are also included.
Author: Maddy Griswold [cre, aut], Nicole Ortogero [aut], Zhi Yang [aut], Ronalyn Vitancol [aut], David Henderson [aut]
Maintainer: Maddy Griswold <mgriswold at nanostring.com>
citation("GeomxTools")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GeomxTools")
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("GeomxTools")| Coercion of GeoMxSet to Seurat and SpatialExperiment Objects | HTML | R Script |
| Developer Introduction to the NanoStringGeoMxSet | HTML | R Script |
| Protein data using GeomxTools | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, DataImport, ExperimentalDesign, GeneExpression, Normalization, ProprietaryPlatforms, Proteomics, RNASeq, Sequencing, Software, Spatial, Transcription, Transcriptomics, mRNAMicroarray |
| Version | 3.17.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | MIT |
| Depends | R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors |
| Imports | BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment(>= 1.4.0), SpatialDecon, patchwork |
| Linking To | |
| Enhances | |
| Depends On Me | GeoMxWorkflows |
| Imports Me | GeoDiff, SpatialDecon, SpatialOmicsOverlay |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GeomxTools_3.17.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | GeomxTools_3.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GeomxTools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GeomxTools |
| Bioc Package Browser | https://code.bioconductor.org/browse/GeomxTools/ |
| Package Short Url | https://bioconductor.org/packages/GeomxTools/ |
| Package Downloads Report | Download Stats |