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 5 months ago

immunooncologyfeatureextractiongeneexpressiontranscriptomicsspatial

32 stars 7.91 score 125 dependencies

GeomxTools - 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 20 days ago

geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseqsequencingexperimentaldesignnormalizationspatial

7.21 score 118 dependencies 3 dependents

NanoStringNCTools - 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 5 months ago

geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseq

6.35 score 79 dependencies 4 dependents

SpatialOmicsOverlay - 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 5 months ago

geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsproprietaryplatformsrnaseqspatialdatarepresentationvisualization

3.54 score 159 dependencies