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 3 weeks ago
• nf-core / spatialxe
  ☆19Updated 3 weeks ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• nf-core / imcyto
  Image Mass Cytometry analysis pipeline
  ☆27Updated 2 months 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
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆27Updated 10 months ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆38Updated 2 months ago
• 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
• BodenmillerGroup / imctools
  Tools to handle IMC data
  ☆23Updated 3 years ago
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆111Updated this week
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆15Updated 3 months ago
• 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
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆24Updated last year
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆34Updated last week
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆29Updated this week
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆39Updated 3 weeks ago
• scverse / spatialdata-notebooks
  ☆54Updated last week
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆80Updated last week
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 6 months ago
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆18Updated 6 months ago
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆33Updated 3 weeks ago
• scverse / conference-2024
  Slides and Notebooks for scverse 2024
  ☆17Updated 10 months ago
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆30Updated 8 months ago
• quadbio / cell-annotator
  Automatically annotate cell types, consistently across samples.
  ☆14Updated last week
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆58Updated last month
• rajewsky-lab / spacemake
  ☆44Updated last week
• vitessce / vitessceR
  R API and htmlwidget for Vitessce
  ☆42Updated 9 months ago
• scverse / genomic-features
  Genomic Features in Python from BioConductor's AnnotationHub
  ☆22Updated this week
• haniffalab / webatlas-app
  An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.
  ☆14Updated last year
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆34Updated last month