Alternatives and similar repositories for mcmicro

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

• nf-core / molkart
  A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
  ☆13Updated last month
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• nf-core / imcyto
  Image Mass Cytometry analysis pipeline
  ☆26Updated 2 months ago
• nf-core / spatialxe
  ☆20Updated last week
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆28Updated 10 months ago
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆31Updated this week
• 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 3 years ago
• sagar87 / spatialproteomics
  Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…
  ☆32Updated 3 weeks ago
• BodenmillerGroup / imctools
  Tools to handle IMC data
  ☆23Updated 3 years ago
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆64Updated last month
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆39Updated 3 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆40Updated last month
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 7 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆82Updated last month
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆16Updated 3 months ago
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆114Updated last week
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆18Updated 7 months ago
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆59Updated last week
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆50Updated this week
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆30Updated 9 months ago
• scverse / genomic-features
  Genomic Features in Python from BioConductor's AnnotationHub
  ☆22Updated last week
• scverse / spatialdata-io
  ☆68Updated last week
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆35Updated last week
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆33Updated last week
• gerstung-lab / BaSISS
  Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
  ☆26Updated 2 years ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆54Updated 2 months ago
• AllenInstitute / cell_type_mapper
  Repository for storing prototype functionality implementations for the BKP
  ☆33Updated last week
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆38Updated 2 years ago
• scverse / conference-2024
  Slides and Notebooks for scverse 2024
  ☆17Updated 11 months ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆24Updated last year