spatial-transcriptomics topic

List spatial-transcriptomics repositories

decoupler-py

140
Stars
20
Forks
Watchers

Python package to perform enrichment analysis from omics data.

verified publisher icon saezlab

MERINGUE

52
Stars
5
Forks
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characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

verified publisher icon JEFworks-Lab

MERmaid

27
Stars
5
Forks
Watchers

WebGL-based viewer for spatially-resolved transcriptomics data

verified publisher icon JEFworks-Lab

SpiceMix

59
Stars
9
Forks
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spatial transcriptome, single cell

verified publisher icon ma-compbio

BestPracticesST

28
Stars
7
Forks
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'Best Practices for Spatial Transcriptomics Analysis with Bioconductor' online book

verified publisher icon lmweber

spateo-release

147
Stars
23
Forks
Watchers

Spatiotemporal modeling of spatial transcriptomics

verified publisher icon aristoteleo

bulk2space

105
Stars
23
Forks
Watchers

a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles

verified publisher icon ZJUFanLab

SpaTalk

53
Stars
17
Forks
Watchers

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

verified publisher icon ZJUFanLab

spatialvi

40
Stars
12
Forks
Watchers

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

verified publisher icon nf-core

dance

328
Stars
30
Forks
Watchers

DANCE: a deep learning library and benchmark platform for single-cell analysis

verified publisher icon OmicsML