Alternatives and similar repositories for readimc

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

• nolanlab / SpatialScore
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…
  ☆15Updated 4 years ago
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆37Updated last year
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆99Updated 3 months ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆24Updated last year
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆88Updated last year
• ElementoLab / utag
  ☆39Updated last year
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆44Updated this week
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆83Updated 2 months ago
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆38Updated this week
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆33Updated last year
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆38Updated last week
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆64Updated last week
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆67Updated 11 months ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆40Updated 7 months ago
• fish-quant / ComSeg
  comseg
  ☆24Updated 7 months ago
• seqscope / ficture
  ☆37Updated 2 months ago
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆25Updated last week
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆45Updated last year
• nf-core / spatialxe
  ☆21Updated 2 weeks ago
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆18Updated 8 months ago
• BodenmillerGroup / cytomapper
  R package for visualization of highly multiplexed imaging data
  ☆33Updated 4 months ago
• CellProfiling / pipex
  A pipeline to transform images into valuable analysis items
  ☆15Updated 3 months ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆137Updated last week
• SchapiroLabor / histoCAT
  Histology Topography Cytometry Analysis Toolbox
  ☆67Updated 2 years ago
• BodenmillerGroup / IMCDataAnalysis
  R based workflow for multiplexed imaging data
  ☆32Updated 2 months ago
• Feanor007 / MESA
  A python package for Multiomics and Ecological Spatial Analysis (MESA)
  ☆21Updated 5 months ago
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆15Updated 2 years ago
• dpeerlab / ENVI
  ☆51Updated 4 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…
  ☆26Updated last year
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆97Updated 6 months ago