Alternatives and similar repositories for tissue_miner

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

• hms-dbmi / brainmapr
  R package to infer spatial location of neuronal subpopulations within the developing mouse brain by integrating single-cell RNA-seq data …
  ☆16Updated 10 years ago
• alexandrovteam / SpaceM
  ☆15Updated 10 months ago
• nolanlab / vortex
  VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:
  ☆34Updated 2 years ago
• whitews / FlowIO
  A Python library for reading and writing Flow Cytometry Standard (FCS) files
  ☆48Updated 2 months ago
• JEFworks-Lab / MERmaid
  WebGL-based viewer for spatially-resolved transcriptomics data
  ☆28Updated 2 years ago
• blaineylab / OpticalPooledScreens
  ☆13Updated 2 years ago
• nf-core / mcmicro
  An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
  ☆19Updated last week
• GuignardLab / napari-sc3D-viewer
  A plugin to visualise 3D spatial single cell omics
  ☆22Updated last month
• broadinstitute / cell-health
  Predicting Cell Health with Morphological Profiles
  ☆37Updated 3 years ago
• broadchenf / Slideseq
  ☆11Updated 6 years ago
• fmi-basel / glib-nature2018-materials
  Image Processing Package for the Paper "Self-organization and symmetry breaking in intestinal organoid development"
  ☆11Updated 4 years ago
• wahlby-lab / graph-iss
  Graph-based Decoding for In Situ Sequencing
  ☆10Updated 5 years ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• feldman4 / OpticalPooledScreens_2019
  Examples and code for optical pooled screens
  ☆10Updated 2 years ago
• TaylorResearchLab / scedar
  Single-cell exploratory data analysis for RNA-Seq
  ☆40Updated 4 years ago
• BodenmillerGroup / imctools
  Tools to handle IMC data
  ☆23Updated 3 years ago
• saeyslab / FlowSOM_Python
  The complete FlowSOM package known from R, now available in Python!
  ☆22Updated this week
• PreibischLab / STIM
  Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.
  ☆28Updated last month
• theislab / interactive_plotting
  ☆22Updated 4 years ago
• metaspace2020 / metaspace-converter
  Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData
  ☆11Updated last year
• zhiqianZ / supCPM
  The algorithm, supervised Capacity Mapping (supCPM), to visualize scRNA-seq data
  ☆7Updated 10 months ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆53Updated 3 weeks ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆27Updated 9 months ago
• cytomining / cytominer
  Methods for Image-Based Cell Profiling
  ☆51Updated last year
• SofieVG / FlowSOM
  Using self-organizing maps for visualization and interpretation of cytometry data
  ☆64Updated last year
• ggirelli / iFISH-probe-design
  iFISH Probe Design: a Python3 package to build iFISH probes.
  ☆12Updated 3 years ago
• merfishtools / merfishtools
  MERFISHTools implement a Bayesian framework for accurately predicting gene or transcript expression from MERFISH data. On top, they provi…
  ☆14Updated 5 years ago
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆47Updated 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…
  ☆28Updated 2 weeks ago
• YosefLab / FastProject
  Dimensionality reduction for single cell RNA-seq data
  ☆36Updated 5 years ago