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Search results for python spatial transcriptomics

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22 search results found

Squidpy ⭐ 362

Spatial Single Cell Analysis in Python

Tools for computational pathology

DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

Spateo Release ⭐ 135

Spatiotemporal modeling of spatial transcriptomics

Decoupler Py ⭐ 112

Python package to perform enrichment analysis from omics data.

Spatial-Linked Alignment Tool

Interactive software tool for the assignment of cell types in single-cell studies.

Stitch3d ⭐ 27

Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices

Technology-invariant pipeline for spatial-omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells

A probabilistic cell typing algorithm for spatial transcriptomics.

Napari Sc3d Viewer ⭐ 16

A plugin to visualise 3D spatial single cell omics

HoloNet. Reveal the holograph of functional communication events in spatial transcriptomics. Help understand how microenvironments shaping cellular phenotypes

Oligo Designer Toolsuite ⭐ 12

Develop custom oligo design pipelines.

St_gridnet ⭐ 12

A Python implementation of the model described in our publication "A convolutional neural network for common-coordinate registration of high-resolution histology images" developed principally for applications to registration of spatial transcriptomics image data.

Spateo Viewer ⭐ 10

Web application demonstrating 3D modeling of spatial transcriptomics

St_analysis ⭐ 8

A toolset for analysis and visualisation of Spatial Transcriptomics datasets.

Single_cell_spatial_image ⭐ 8

A deep-learning framework for characterizing and visualizing tissue architecture from spatially resolved transcriptomics

Singlecellhaystack Py ⭐ 8

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).

St_pipeline ⭐ 6

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

Generate the UMI count matrix from CEL-Seq2 sequencing data

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