spatial-transcriptomics

There are 37 repositories under spatial-transcriptomics topic.

• squidpy

  scverse / squidpy

  Spatial Single Cell Analysis in Python

  single-cell-rna-seqsingle-cell-genomicsspatial-transcriptomicsspatial-analysisimage-analysisdata-visualizationsquidpy
  Language:Python 529

• jinworks / CellChat

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

  cell-cell-communicationcell-cell-interactionmicroenvironmentsingle-cell-analysisspatial-transcriptomics
  Language:R 487

• smorabit / hdWGCNA

  High dimensional weighted gene co-expression network analysis

  gene-regulatory-networknetwork-analysissingle-cellspatial-transcriptomics
  Language:R 441
• pathml

  Dana-Farber-AIOS / pathml

  Tools for computational pathology

  biomedical-image-processingcomputational-pathologydeep-learningdigital-pathologyfluorescence-microscopy-imaginghistopathologyimage-analysismachine-learningmicroscopypathmlpathologypythonpytorchresearchspatial-transcriptomics
  Language:Python 438

• dmcable / spacexr

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

  spatial-transcriptomicsdifferential-expressioncell-type-identification
  Language:HTML 406

• OmicsML / dance

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

  bioinformaticsdancedata-sciencedeep-learninggraph-neural-networksmachine-learningmultimodalitypythonsingle-cellspatial-transcriptomicsbenchmarkcomputational-biologysingle-cell-rna-seqsingle-cell-rna-sequencing
  Language:Python 384

• mahmoodlab / HEST

  Integrating histology and spatial transcriptomics - NeurIPS 2024

  spatial-transcriptomicscomputational-pathologyhistology
  Language:Python 330

• aristoteleo / spateo-release

  Spatiotemporal modeling of spatial transcriptomics

  3d-reconstructioncell-segmentationspatial-transcriptomicsspatiotemporal
  Language:Python 318

• jianhuupenn / SpaGCN

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

  spatial-transcriptomicsgraph-convolutional-networkspatial-domainsspatially-variable-genes
  Language:Python 243

• gustaveroussy / sopa

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

  spatial-omicsspatial-transcriptomicsspatialdatamultiplexed-imagingpipelinesegmentation
  Language:Python 242

• scverse / decoupler

  Python package to perform enrichment analysis from omics data.

  pythondata-sciencebioinformaticstranscriptomicsnumbasingle-cellspatial-transcriptomicsenrichmentenrichment-analysis
  Language:Python 236

• aristoteleo / pantheon-cli

  Pantheon-CLI, our first release of PantheonOS, the AgentOS that re-imagines Science

  agentagentosclipantheonossinglecellspatial-transcriptomics
  Language:Python 211

• kharchenkolab / numbat

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

  cancer-genomicscnv-detectionsingle-cellphylogenysingle-cell-analysissingle-cell-rna-seqspatial-transcriptomicslineage-tracing
  Language:R 198

• kharchenkolab / Baysor

  Bayesian Segmentation of Spatial Transcriptomics Data

  spatial-transcriptomicssegmentationbayesianxenium
  Language:Julia 196

• JianYang-Lab / gsMap

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

  gwasspatial-transcriptomicsbioinformatics-toolspatial-dataspatial-data-analysisstatistical-genetics
  Language:Python 184

• theMILOlab / SPATA2

  A Toolbox for Spatial Transcriptomics Analysis

  data-analysisimage-analysisspatial-omicsspatial-transcriptomics
  Language:R 159

• ZJUFanLab / bulk2space

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

  bulk-sequencingdeep-learningscrna-seqspatial-transcriptomics
  Language:Jupyter Notebook 126

• rajewsky-lab / openst

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

  bioinformaticsomicsspatial-transcriptomicstranscriptomics
  Language:HTML 106

• 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"

  spatial-transcriptomicsvisiumhd
  Language:R 100

• LieberInstitute / spatialLIBD

  Code for the spatialLIBD R/Bioconductor package and shiny app

  rstatsshinyspatial-transcriptomics10xgenomicsbioconductorgolemvisiumspatialexperimentspatiallibd
  Language:R 100

• pachterlab / voyager

  From geospatial to spatial -omics

  bioconductoredaesdaexploratory-data-analysisomicsrr-packagerstatsspatialspatial-statisticsspatial-transcriptomicstranscriptomics
  Language:R 98

• lmweber / OSTA

  "Orchestrating Spatial Transcriptomics Analysis with Bioconductor" book

  spatially-resolved-transcriptomicsbioconductorspatial-transcriptomicsanalysis-workflows
  Language:TeX 92
• SLAT

  gao-lab / SLAT

  Spatial-Linked Alignment Tool

  bioinformaticssingle-cellspatial-dataspatial-transcriptomicssingle-cell-analysisdeep-learninggraph-neural-networks
  Language:Python 89

• 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.

  pipelinespatial-transcriptomicsvisiumscrna-seq
  Language:Python 88

• alexisvdb / singleCellHaystack

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

  bioinformaticssingle-cellrtranscriptomicsspatial-transcriptomicscite-seqpseudotimescatac-seqspatial-proteomics
  Language:R 85

• LieberInstitute / HumanPilot

  Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

  spatial-transcriptomicsrstats10xgenomicsvisiumdlpfchumanbrainanalysisbiorxiv
  Language:HTML 85

• JEFworks-Lab / MERINGUE

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

  single-cellspatial-analysisspatial-transcriptomicsgene-expressionrstatscell-cell-communication
  Language:R 81
• Spatial_transcriptomics_tools

  p-gueguen / Spatial_transcriptomics_tools

  List of Spatial Transcriptomics related Tools organized per category

  pathologysingle-cell-analysisspatial-transcriptomics
  Language:Python 81

• EliHei2 / segger_dev

  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).

  aicell-segmentationgraph-neural-networksgraphsoncologysegmentationsingle-cell-analysisspatial-omicsspatial-transcriptomicsxeniummolecule-graphs
  Language:HTML 79

• ZJUFanLab / SpaTalk

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

  cell-cell-communicationcell-cell-interactionknowledge-graphspatial-data-analysisligand-receptor-interactiongraph-networkspatially-resolved-transcriptomicsspatial-transcriptomicssingle-cell
  Language:R 72

• ma-compbio / SpiceMix

  spatial transcriptome, single cell

  spatial-transcriptomicssingle-cellmachine-learning
  Language:Jupyter Notebook 71

• saezlab / mistyR

  Multiview Intercellular SpaTial modeling framework

  multiviewintercellularspatialmodularbiologymolecular-biologyrspatial-transcriptomicsmachine-learningbioconductor
  Language:R 71

• YangLabHKUST / STitch3D

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

  3d-reconstructionspatial-transcriptomicsdeep-learning
  Language:Python 69

• nf-core / spatialvi

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

  nf-corenextflowworkflowpipeline10x-genomics10xgenomicsbioinformaticsimage-processingmicroscopyrna-seqsingle-cellspatialspatial-transcriptomicssttranscriptomicsvisium
  Language:Nextflow 67

• 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.

  cell-cell-communicationglioblastomalarge-scale-data-analyticssingle-cell-rna-seqspatial-transcriptomics
  Language:Jupyter Notebook 64

• genecell / COSGR

  Accurate and fast cell marker gene identification with COSG

  scrna-seqscatac-seqspatial-transcriptomicsmarker-genes
  Language:R 62