Alternatives and similar repositories for imcyto

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

• BodenmillerGroup / imctools
  Tools to handle IMC data
  ☆24Updated 3 years ago
• nf-core / mcmicro
  An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
  ☆27Updated last week
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆65Updated 5 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…
  ☆16Updated 4 years ago
• nf-core / spatialxe
  ☆24Updated last month
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆44Updated 7 months ago
• SchapiroLabor / histoCAT
  Histology Topography Cytometry Analysis Toolbox
  ☆69Updated last month
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆56Updated 6 months ago
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 2 months ago
• ElementoLab / utag
  ☆40Updated last year
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆51Updated 3 years ago
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆15Updated 2 years ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆84Updated last month
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆33Updated 2 weeks ago
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆29Updated last year
• lilab-bcb / cirrocumulus
  Bring your single-cell data to life
  ☆89Updated 2 weeks ago
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆109Updated last month
• rajewsky-lab / spacemake
  ☆48Updated this week
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆105Updated last week
• theislab / troutpy
  Package for the analysis of Transcripts outside segmented cells in ST data
  ☆23Updated this week
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆30Updated last year
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆64Updated 2 weeks ago
• SpatialTranscriptomicsResearch / st_spot_detector
  A web tool to do automatic spots detections and positional adjustments for Spatial Transcriptomics Datasets.
  ☆25Updated 3 years ago
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆38Updated last year
• MacoskoLab / slideseq-tools
  Tools for analyzing Slide-seq data
  ☆31Updated 2 years ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆47Updated last month
• nf-core / spatialvi
  Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…
  ☆69Updated last month
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆144Updated this week
• Nanostring-Biostats / SpatialDecon
  The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…
  ☆41Updated this week