camlab-bioml / astir

Related projects ⓘ

Alternatives and complementary repositories for astir

• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆23Updated last month
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆30Updated 6 months ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆74Updated this week
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆24Updated 2 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆70Updated 2 weeks ago
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆45Updated last week
• shuxiaoc / mario-py
  MARIO: single-cell proteomic data matching and integration using both shared and distinct features
  ☆21Updated last year
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆92Updated last week
• BiomedicalMachineLearning / Spacell
  ☆25Updated 5 years ago
• scverse / spatialdata-io
  ☆43Updated last week
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆29Updated 10 months ago
• theislab / interactive_plotting
  ☆21Updated 4 years ago
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆35Updated last year
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆16Updated 3 months ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆69Updated 11 months ago
• nf-core / imcyto
  Image Mass Cytometry analysis pipeline
  ☆25Updated last month
• ElementoLab / utag
  ☆33Updated 7 months ago
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆50Updated 2 weeks ago
• AI4SCR / ATHENA
  ☆31Updated last month
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆38Updated 3 years ago
• scverse / spatialdata-notebooks
  ☆38Updated last week
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆59Updated 2 years ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆25Updated this week
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆27Updated this week
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆20Updated 3 months ago
• BIMSBbioinfo / VoltRon
  Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration
  ☆41Updated this week
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆42Updated 2 years ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆40Updated 4 months ago
• YosefLab / PopV
  ☆23Updated 2 months ago
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆44Updated this week