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.
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immunooncologyfeatureextractiongeneexpressiontranscriptomicsspatial
7.78 score 44 stars 115 scripts 685 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.
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geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseqsequencingexperimentaldesignnormalizationspatial
7.23 score 5 dependents 316 scripts 1.2k 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.
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geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseq
6.54 score 6 dependents 176 scripts 1.1k downloadsGeoDiff - Count model based differential expression and normalization on GeoMx RNA data
A series of statistical models using count generating distributions for background modelling, feature and sample QC, normalization and differential expression analysis on GeoMx RNA data. The application of these methods are demonstrated by example data analysis vignette.
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geneexpressiondifferentialexpressionnormalizationopenblascppopenmp
6.00 score 9 stars 22 scripts 426 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.
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geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsproprietaryplatformsrnaseqspatialdatarepresentationvisualizationopenjdk
4.46 score 29 scripts 426 downloadsGeoMxWorkflows - GeoMx Digital Spatial Profiler (DSP) data analysis workflows
Workflows for use with NanoString Technologies GeoMx Technology. Package provides bioconductor focused workflows for leveraging existing packages (e.g. GeomxTools) to process, QC, and analyze the data.
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geneexpressionworkflowimmunooncologyworkflowspatialworkflow
3.00 score