Alternatives and similar repositories for SPIAT:

Users that are interested in SPIAT are comparing it to the libraries listed below

• walsh-quail-labs / IMC_Brain
  ☆18Updated last year
• wanglab-broad / CAST
  CAST package
  ☆34Updated 5 months ago
• Banovich-Lab / Spatial_PF
  ☆24Updated last month
• jbergenstrahle / STUtility
  ☆49Updated 2 years ago
• nolanlab / SpatialScore
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…
  ☆14Updated 3 years ago
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆26Updated 8 months ago
• FridleyLab / spatialGE
  Methods for visualization and analysis of spatially-resolved gene expression
  ☆17Updated this week
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆33Updated this week
• BodenmillerGroup / imcRtools
  An R package for handling and analysing imaging mass cytometry data
  ☆24Updated 5 months ago
• kaishumason / NicheDE
  NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.
  ☆17Updated 6 months ago
• QihuangZhang / CeLEry
  CeLEry: cell location recovery in single-cell RNA sequencing
  ☆34Updated 2 months ago
• saezlab / MOFAcellulaR
  R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)
  ☆10Updated last year
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆16Updated last year
• CamaraLab / ConDecon
  R package: ConDecon is a clustering-independent deconvolution method for estimating cell abundances in bulk tissues using single-cell RNA…
  ☆12Updated 5 months ago
• tanlabcode / CytoCommunity
  The first computational tool that enables both unsupervised and supervised discovery of tissue spatial domains
  ☆27Updated this week
• davidliwei / PS
  Perturbation-response Score (PS) analysis is a method to quantify diverse perturbation responses and discover novel biological insights i…
  ☆12Updated 11 months ago
• liuqivandy / SpaGene
  ☆19Updated last year
• YingMa0107 / IRIS
  Integrative and Reference-Informed Spatial Domain Detection for Spatial Transcriptomics
  ☆34Updated 2 months ago
• 10XGenomics / janesick_nature_comms_2023_companion
  Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spat…
  ☆18Updated last year
• ding-lab / mushroom
  A computational tool for identification of 3D multi-modal spatial neighborhoods
  ☆11Updated 2 months ago
• MargoKapustina / XeniumSpatialAnalysis
  R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients
  ☆17Updated 2 weeks ago
• dchary / ucdeconvolve
  UniCell Deconvolve - Cloud Cell Type Deconvolution For Transcriptomic Data
  ☆24Updated last year
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆26Updated 3 months ago
• bsungwoo / spSeudoMap
  spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data
  ☆12Updated 6 months ago
• Teichlab / visium_stitcher
  Stitch multiple Visium slides together
  ☆15Updated last year
• azizilab / DIISCO_public
  Publically accessible code for DIISCO method
  ☆10Updated 5 months ago
• shenglinmei / ProstateCancerAnalysis
  ☆17Updated last month
• ZJUFanLab / CellTalkDB
  A manually curated database of literature-supported ligand-receptor interactions in human and mouse
  ☆30Updated 9 months ago
• welch-lab / cytosignal
  ☆17Updated this week
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆26Updated 6 months ago