This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GeomxTools.
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 (from within R,
enter citation("GeomxTools")
):
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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GeomxTools")
HTML | R Script | Coercion of GeoMxSet to Seurat and SpatialExperiment Objects |
HTML | R Script | Developer Introduction to the NanoStringGeoMxSet |
HTML | R Script | Protein data using GeomxTools |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
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) (2 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 |
LinkingTo | |
Suggests | rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment(>= 1.4.0), SpatialDecon, patchwork |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | GeoMxWorkflows |
Imports Me | GeoDiff, SpatialDecon |
Suggests Me | |
Links To Me | |
Build Report |
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 |
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