SpatialDecon - Deconvolution of mixed cells from spatial and/or bulk gene expression data
Using spatial or bulk gene expression data, estimates abundance of mixed cell types within each observation. Based on "Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data", Danaher (2022). Designed for use with the NanoString GeoMx platform, but applicable to any gene expression data.
Last updated 2 months ago
immunooncologyfeatureextractiongeneexpressiontranscriptomicsspatial
7.75 score 33 stars 57 scripts 388 downloadsGeomxTools - NanoString GeoMx Tools
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.
Last updated 2 months ago
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseqsequencingexperimentaldesignnormalizationspatial
7.25 score 3 dependents 219 scripts 754 downloadsNanoStringNCTools - NanoString nCounter Tools
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.
Last updated 2 months ago
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseq
6.44 score 4 dependents 91 scripts 642 downloadsSpatialOmicsOverlay - Spatial Overlay for Omic Data from Nanostring GeoMx Data
Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.
Last updated 2 months ago
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsproprietaryplatformsrnaseqspatialdatarepresentationvisualizationopenjdk
4.40 score 8 scripts 176 downloads