Alternatives and similar repositories for molkart

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

• nf-core / mcmicro
  An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
  ☆30Updated this week
• sagar87 / spatialproteomics
  Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…
  ☆39Updated last month
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆66Updated 6 months ago
• nf-core / spatialxe
  ☆24Updated last month
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆34Updated last year
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 3 months ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆46Updated 8 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆86Updated 2 months ago
• broadinstitute / celldega
  Spatial omics analysis and visualization library
  ☆22Updated last week
• nf-core / imcyto
  Image Mass Cytometry analysis pipeline
  ☆26Updated 7 months ago
• theislab / troutpy
  Package for the analysis of Transcripts outside segmented cells in ST data
  ☆24Updated last week
• scverse / ecosystem-packages
  Registry for scverse ecosystem packages
  ☆32Updated this week
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• SydneyBioX / MoleculeExperiment
  ☆12Updated last year
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆30Updated last year
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆65Updated this week
• scverse / genomic-features
  Genomic Features in Python from BioConductor's AnnotationHub
  ☆22Updated last week
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆33Updated this week
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆146Updated last month
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆48Updated 2 months ago
• BodenmillerGroup / imctools
  Tools to handle IMC data
  ☆24Updated 3 years ago
• scverse / spatialdata-notebooks
  ☆64Updated this week
• scverse / spatialdata-io
  ☆87Updated last week
• theislab / multimil
  Weakly supervised learning uncovers phenotypic signatures in single-cell data
  ☆38Updated last month
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆16Updated 4 months ago
• vitessce / vitessceR
  R API and htmlwidget for Vitessce
  ☆43Updated 5 months ago
• haniffalab / webatlas-app
  An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.
  ☆14Updated 2 months ago
• rajewsky-lab / spacemake
  ☆48Updated this week
• DendrouLab / panpipes
  Multi-modal single cell analysis pipelines
  ☆62Updated last month
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆51Updated this week