GeomxTools
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GeomxTools.
NanoString GeoMx Tools
Bioconductor version: 3.16
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: Nicole Ortogero [cre, aut], Zhi Yang [aut], Ronalyn Vitancol [aut], Maddy Griswold [aut], David Henderson [aut]
Maintainer: Nicole Ortogero <nortogero at nanostring.com>
citation("GeomxTools")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 3.2.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 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 |
| 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_3.2.0.tar.gz |
| Windows Binary | GeomxTools_3.2.0.zip |
| macOS Binary (x86_64) | GeomxTools_3.2.0.tgz |
| macOS Binary (arm64) | GeomxTools_3.2.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |