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)
  ☆12Updated last week
• nf-core / spatialxe
  ☆19Updated last week
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆27Updated 9 months ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated 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…
  ☆14Updated 3 years ago
• nf-core / imcyto
  Image Mass Cytometry analysis pipeline
  ☆26Updated last month
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆14Updated 2 months ago
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆63Updated last week
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆30Updated last week
• sagar87 / spatialproteomics
  Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…
  ☆28Updated last week
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆18Updated 6 months ago
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆29Updated last month
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 6 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆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.
  ☆27Updated 9 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆80Updated 3 weeks ago
• BodenmillerGroup / imctools
  Tools to handle IMC data
  ☆23Updated 3 years ago
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆105Updated last week
• HelenaLC / SpatialData
  ☆17Updated last month
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆23Updated 11 months ago
• vitessce / vitessceR
  R API and htmlwidget for Vitessce
  ☆41Updated 9 months ago
• Mr-Milk / SpatialTis
  Spatial analysis toolkit for single cell multiplexed tissue data
  ☆30Updated 10 months ago
• vitessce / vitessce-python
  Python API and Jupyter widget for Vitessce
  ☆49Updated this week
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆37Updated last month
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆47Updated this week
• scverse / conference-2024
  Slides and Notebooks for scverse 2024
  ☆17Updated 9 months ago
• satijalab / panhumanpy
  ☆17Updated 2 months ago
• scverse / spatialdata-io
  ☆63Updated 2 weeks ago
• buettnerlab / convexgating
  Optimal gating strategies for flow and mass cytometry.
  ☆13Updated 3 months ago
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆33Updated this week