Alternatives and similar repositories for ImagingWorkshop2023

Users that are interested in ImagingWorkshop2023 are comparing it to the libraries listed below

• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆53Updated 3 years ago
• BIMSBbioinfo / VoltRon
  Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration
  ☆114Updated 2 weeks ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆146Updated 2 years ago
• saezlab / visium_heart
  Spatial transcriptomics of heart tissue
  ☆103Updated 2 years ago
• shuxiaoc / maxfuse
  ☆56Updated last year
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆151Updated 4 months ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆145Updated last week
• yuqiyuqitan / SPACEc
  ☆55Updated last week
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆130Updated last month
• elixir-europe-training / ELIXIR-SCO-spatial-omics
  ☆45Updated 8 months ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆137Updated 9 months ago
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆81Updated 3 years ago
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆115Updated last year
• Nanostring-Biostats / CosMx-Analysis-Scratch-Space
  This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…
  ☆86Updated last week
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆70Updated last year
• ruppinlab / PERCEPTION
  Utilizing single-cell omics from patients tumor to predict response and resistance.
  ☆71Updated 2 years ago
• navinlabcode / CellTrek
  ☆126Updated 3 years ago
• azizilab / starfysh
  Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology
  ☆127Updated 6 months ago
• omnideconv / omnideconv
  Unified access to several second-generation deconvolution methods
  ☆88Updated last month
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆51Updated 3 years ago
• YMa-lab / CARD
  ☆129Updated last year
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆130Updated 2 months ago
• matanhofree / crc-immune-hubs
  Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…
  ☆38Updated 4 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆172Updated 8 months ago
• BodenmillerGroup / imcRtools
  An R package for handling and analysing imaging mass cytometry data
  ☆29Updated last month
• favilaco / deconv_benchmark
  ☆59Updated 5 years ago
• YosefLab / Compass
  In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
  ☆117Updated last month
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆226Updated last year
• 10XGenomics / HumanColonCancer_VisiumHD
  Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…
  ☆104Updated 6 months ago
• Sanofi-Public / enact-pipeline
  Repository for ENACT pipeline for end-to-end analysis of Visium HD data
  ☆71Updated 6 months ago