Alternatives and similar repositories for profiling-handbook

Users that are interested in profiling-handbook are comparing it to the libraries listed below

• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆65Updated 6 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆86Updated last month
• DendrouLab / panpipes
  Multi-modal single cell analysis pipelines
  ☆62Updated last month
• BIMSBbioinfo / VoltRon
  Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration
  ☆114Updated this week
• bfurtwa / SCeptre
  SCeptre is a python package that extends the functionalities of Scanpy to analyze multiplexed single-cell proteomics data.
  ☆18Updated last year
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆145Updated 3 weeks ago
• scverse / spatialdata-notebooks
  ☆64Updated this week
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆33Updated 3 weeks ago
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆34Updated last year
• saezlab / mistyR
  Multiview Intercellular SpaTial modeling framework
  ☆71Updated 7 months ago
• scverse / spatialdata-io
  ☆86Updated this week
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆49Updated this week
• yuqiyuqitan / SPACEc
  ☆58Updated last month
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆106Updated this week
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆47Updated 2 months ago
• prabhakarlab / Banksy_py
  BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …
  ☆72Updated last month
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆19Updated last year
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆15Updated 2 years ago
• SpatialHackathon / SACCELERATOR
  ☆28Updated 3 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 3 weeks ago
• carpenter-singh-lab / 2022_Haghighi_NatureMethods
  High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
  ☆52Updated 5 months ago
• AllenInstitute / cell_type_mapper
  Repository for storing prototype functionality implementations for the BKP
  ☆39Updated last month
• BorchLab / Ibex
  Using BCR and expression for sequence embedding
  ☆25Updated last month
• 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…
  ☆89Updated 2 weeks ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆56Updated 6 months ago
• theislab / multimil
  Weakly supervised learning uncovers phenotypic signatures in single-cell data
  ☆38Updated 3 weeks ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆69Updated 2 months ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 8 months ago
• nf-core / mcmicro
  An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
  ☆29Updated 3 weeks ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆147Updated last month