Alternatives and similar repositories for CosMx_Lite

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

• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆25Updated last year
• nolanlab / SpatialScore
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…
  ☆16Updated 4 years ago
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆16Updated 3 months ago
• bdsc-tds / SPLIT
  Profile purification of single-cell spatial transcriptomics data
  ☆26Updated last month
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆33Updated last week
• welch-lab / cytosignal
  ☆21Updated last week
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆19Updated 11 months ago
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆48Updated last week
• BodenmillerGroup / IMCDataAnalysis
  R based workflow for multiplexed imaging data
  ☆36Updated 5 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…
  ☆29Updated 2 years ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆105Updated last week
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆38Updated last year
• Nanostring-Biostats / FastReseg
  FastReseg for detection and correction of cell segmentation error based on spatial profile of transcripts.
  ☆12Updated 2 weeks ago
• dchary / ucdeconvolve
  UniCell Deconvolve - Cloud Cell Type Deconvolution For Transcriptomic Data
  ☆26Updated 2 years ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆47Updated last month
• nf-core / spatialxe
  ☆24Updated last month
• pekjoonwu / CELINA
  ☆17Updated last year
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆93Updated 2 years ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆41Updated 9 months ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆38Updated last month
• bhuvad / SpaNorm
  R package for normalisation of spatial transcriptomics data
  ☆15Updated 6 months ago
• LiHongCSBLab / SOAPy
  ☆31Updated 10 months ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆130Updated last month
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆72Updated last year
• joshwillmoore1 / MuSpAn-Public
  A public MuSpAn page for community discussions and issue reporting.
  ☆18Updated 2 months ago
• damienArnol / svca
  ☆13Updated 6 years ago
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆35Updated last year
• Wei-BioMath / NeuronChat
  ☆41Updated 2 years ago
• seqscope / ficture
  ☆42Updated 2 months ago
• theislab / troutpy
  Package for the analysis of Transcripts outside segmented cells in ST data
  ☆23Updated this week