GeomxTools
NanoString GeoMx Tools
Bioconductor version: 3.23 · Package version: 3.16.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GeomxTools")Details
| Maintainer | Maddy Griswold <mgriswold@nanostring.com> |
| Author | Maddy Griswold [cre, aut], Nicole Ortogero [aut], Zhi Yang [aut], Ronalyn Vitancol [aut], David Henderson [aut] |
| License | MIT |
| Downloads rank | 680 |
| Source branch | RELEASE_3_23 |
| biocViews | CellBasedAssays, DataImport, ExperimentalDesign, GeneExpression, Normalization, ProprietaryPlatforms, Proteomics, RNASeq, Sequencing, Software, Spatial, Transcription, Transcriptomics, mRNAMicroarray |
Documentation
- Coercion of GeoMxSet to Seurat and SpatialExperiment Objects
- Developer Introduction to the NanoStringGeoMxSet
- Protein data using GeomxTools
Download
Dependencies
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
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork
Reverse dependencies
Depends On Me (1): GeoMxWorkflows
Imports Me (3): GeoDiff, SpatialDecon, SpatialOmicsOverlay