Alternatives and similar repositories for phenoptr:

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

• 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
• Nanostring-Biostats / SpatialOmicsOverlay
  Tools for analyzing data on the image from NanoString GeoMx Digital Spatial Profiler (DSP).
  ☆18Updated last month
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆23Updated 3 months ago
• jbergenstrahle / STUtility
  ☆47Updated last year
• CamaraLab / STvEA
  Spatially-resolved Transcriptomics via Epitope Anchoring
  ☆18Updated 9 months ago
• BodenmillerGroup / imctools
  Tools to handle IMC data
  ☆23Updated 2 years ago
• BodenmillerGroup / imcRtools
  An R package for handling and analysing imaging mass cytometry data
  ☆22Updated 2 months ago
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆45Updated 2 years ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆33Updated last month
• miccec / GBMstates
  Scripts from the GBM cellular states paper
  ☆18Updated 3 years ago
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆50Updated 2 weeks ago
• SchapiroLabor / histoCAT
  Histology Topography Cytometry Analysis Toolbox
  ☆66Updated last year
• nolanlab / vortex
  VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:
  ☆34Updated last year
• BodenmillerGroup / cytomapper
  R package for visualization of highly multiplexed imaging data
  ☆31Updated 6 months ago
• TrigosTeam / SPIAT
  ☆21Updated 4 months ago
• ElementoLab / utag
  ☆33Updated 9 months ago
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆54Updated 2 months ago
• walsh-quail-labs / IMC-Lung
  ☆16Updated last year
• klarman-cell-observatory / hdst
  ☆19Updated 5 years ago
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆25Updated 3 months ago
• cancer-evolution / SPIAT
  Spatial Image Analysis of Tissues
  ☆15Updated 2 years ago
• BodenmillerGroup / readimc
  Python package for reading imaging mass cytometry (IMC) files
  ☆13Updated this week
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆28Updated 2 months ago
• BodenmillerGroup / IMCDataAnalysis
  R based workflow for multiplexed imaging data
  ☆28Updated 11 months ago
• kaishumason / NicheDE
  NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.
  ☆14Updated 3 months ago
• ElementoLab / imc
  A package for the analysis of Imaging Mass Cytometry data
  ☆13Updated last year
• theMILOlab / SPATA
  SPATA Package for spatial gene expression analysis
  ☆21Updated 2 years ago
• SpatialTranscriptomicsResearch / std-nb
  Negative binomial regression for Spatial Transcriptomics data as described in Maaskola et al. 2018
  ☆21Updated 6 years ago
• nolanlab / TissueSchematics
  Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"
  ☆10Updated last year