spatial-transcriptomics

There are 188 repositories under spatial-transcriptomics topic.

  • squidpy

    scverse/squidpy

    Spatial Single Cell Analysis in Python

    Language:Python5121155098

  • jinworks/CellChat

    R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

    Language:R456232278
  • pathml

    Dana-Farber-AIOS/pathml

    Tools for computational pathology

    Language:Python4381220687

  • dmcable/spacexr

    Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

    Language:HTML3951121585

  • smorabit/hdWGCNA

    High dimensional weighted gene co-expression network analysis

    Language:R395434637

  • OmicsML/dance

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

    Language:Python37664238

  • aristoteleo/spateo-release

    Spatiotemporal modeling of spatial transcriptomics

    Language:Python313517141

  • mahmoodlab/HEST

    Integrating histology and spatial transcriptomics - NeurIPS 2024

    Language:Python31045435

  • jianhuupenn/SpaGCN

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

    Language:Python23518164

  • gustaveroussy/sopa

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

    Language:Python226816836

  • kharchenkolab/Baysor

    Bayesian Segmentation of Spatial Transcriptomics Data

    Language:Julia192714734

  • kharchenkolab/numbat

    Haplotype-aware CNV analysis from single-cell RNA-seq

    Language:R190920025

  • saezlab/decoupler-py

    Python package to perform enrichment analysis from omics data.

    Language:Python189514128

  • JianYang-Lab/gsMap

    Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

    Language:Python18122210

  • theMILOlab/SPATA2

    A Toolbox for Spatial Transcriptomics Analysis

    Language:R138514520

  • ZJUFanLab/bulk2space

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

    Language:Jupyter Notebook12642123

  • rajewsky-lab/openst

    Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

    Language:HTML10583619

  • LieberInstitute/spatialLIBD

    Code for the spatialLIBD R/Bioconductor package and shiny app

    Language:R96198823

  • pachterlab/voyager

    From geospatial to spatial -omics

    Language:R9645313
  • SLAT

    gao-lab/SLAT

    Spatial-Linked Alignment Tool

    Language:Python8821410

  • lmweber/OSTA

    "Orchestrating Spatial Transcriptomics Analysis with Bioconductor" book

    Language:TeX8796925

  • jfnavarro/st_pipeline

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

    Language:Python8651251

  • LieberInstitute/HumanPilot

    Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

    Language:HTML8317931

  • alexisvdb/singleCellHaystack

    Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

    Language:R81589

  • JEFworks-Lab/MERINGUE

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

    Language:R803156

  • ZJUFanLab/SpaTalk

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

    Language:R7235219

  • ma-compbio/SpiceMix

    spatial transcriptome, single cell

    Language:Jupyter Notebook69357

  • saezlab/mistyR

    Multiview Intercellular SpaTial modeling framework

    Language:R6722211

  • nf-core/spatialvi

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

    Language:Nextflow651783422

  • ccruizm/GBmap

    Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.

    Language:Jupyter Notebook616512

  • YangLabHKUST/STitch3D

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

    Language:Python614364

  • genecell/COSGR

    Accurate and fast cell marker gene identification with COSG

    Language:R59158

  • 10XGenomics/HumanColonCancer_VisiumHD

    Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"

    Language:R58564
  • beyondcell

    cnio-bu/beyondcell

    Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.

    Language:R531904

  • jianhuupenn/TESLA

    Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA

    Language:Jupyter Notebook5322513

  • PMBio/segger

    a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).

    Language:Python46