Biocview "Spatial"

Nanostring-Biostats/NanoStringExperiment

Base NanoString Experiment Class

vitessce/vitessce-htmlwidget

Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library

vitessce/vitessce-r

Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library

vitessce/vitessceR

Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library

keller-mark/vitessce-htmlwidget

Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library

FertigLab/scatterHatch

Creates hatched patterns for scatterplots

Nanostring-Biostats/SpatialDecon

Deconvolution of mixed cells from spatial and/or bulk gene expression data

sthawinke/pengls

Fit Penalised Generalised Least Squares models

zhangjunpeng411/miRsponge

Identification and analysis of miRNA sponge regulation

zhangjunpeng411/miRspongeR

Identification and analysis of miRNA sponge regulation

jingeyu/CTSV

Identification of cell-type-specific spatially variable genes accounting for excess zeros

pachterlab/SpatialFeatureExperiment

Integrating SpatialExperiment with Simple Features in sf

BodenmillerGroup/imcRtools

Methods for imaging mass cytometry data analysis

saezlab/misty

Multiview Intercellular SpaTial modeling framework

saezlab/mistyR

Multiview Intercellular SpaTial modeling framework

Nanostring-Biostats/GeomxTools

NanoString GeoMx Tools

JEFworks-Lab/STdeconvolve

Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data

drighelli/SpatialExperiment

S4 Class for Spatially Resolved -omics Data

drighelli/VisiumExperiment

S4 Class for Spatially Resolved -omics Data

lmweber/nnSVG

Scalable identification of spatially variable genes in spatially-resolved transcriptomics data

SydneyBioX/scFeatures

scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

ellispatrick/spicyR

Spatial analysis of in situ cytometry data

data2intelligence/SpaCE

Spatial Cellular Estimator for Tumors

jianhaizhang/spatialHeatmap

spatialHeatmap

TrigosTeam/SPIAT

Spatial Image Analysis of Tissues

Nanostring-Biostats/SpatialOmicsOverlay

Spatial Overlay for Omic Data from Nanostring GeoMx Data

TrigosTeam/spaSim

Spatial point data simulator for tissue images

DavisLaboratory/standR

Spatial transcriptome analyses of Nanostring's DSP data in R

prabhakarlab/Banksy

Spatial transcriptomic clustering

zijianni/SpotClean

SpotClean adjusts for spot swapping in spatial transcriptomics data

MarcElosua/SPOTlight

`SPOTlight`: Spatial Transcriptomics Deconvolution

Nina-Song/stJoincount

stJoincount - Join count statistic for quantifying spatial correlation between clusters

liuwd15/tomoda

Tomo-seq data analysis

lmweber/ggspavis

Visualization functions for spatial transcriptomics data