Alternatives and similar repositories for spatial-transcriptomics-pipeline

Users that are interested in spatial-transcriptomics-pipeline are comparing it to the libraries listed below

• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆86Updated 2 months ago
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆66Updated 7 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆48Updated 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…
  ☆39Updated last month
• nf-core / imcyto
  Image Mass Cytometry analysis pipeline
  ☆26Updated 8 months ago
• scverse / spatialdata-io
  ☆88Updated this week
• nf-core / mcmicro
  An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
  ☆30Updated this week
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆45Updated 7 months ago
• HiDiHlabs / ssam
  ☆27Updated last year
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆25Updated 2 months ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆25Updated last year
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆33Updated last week
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆105Updated last week
• theislab / troutpy
  Package for the analysis of Transcripts outside segmented cells in ST data
  ☆25Updated last week
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆51Updated this week
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆108Updated 3 weeks ago
• vitessce / vitessce-python
  Python API and Jupyter widget for Vitessce
  ☆60Updated last week
• scverse / spatialdata-notebooks
  ☆65Updated this week
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 3 months ago
• nf-core / spatialxe
  ☆24Updated last week
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆65Updated last week
• 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
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆75Updated this week
• ElementoLab / utag
  ☆41Updated last week
• BodenmillerGroup / imctools
  Tools to handle IMC data
  ☆24Updated 3 years ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆56Updated 7 months ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆30Updated last year
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆39Updated 4 months ago
• MICS-Lab / scyan
  Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effe…
  ☆42Updated last year
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆46Updated 8 months ago