Alternatives and similar repositories for bento-tools

Users that are interested in bento-tools are comparing it to the libraries listed below

• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆107Updated last week
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆48Updated 2 months ago
• scverse / spatialdata-io
  ☆87Updated this week
• scverse / spatialdata-notebooks
  ☆64Updated this week
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆35Updated last year
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆51Updated this week
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆104Updated this week
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆94Updated 2 years ago
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆65Updated this week
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆46Updated 7 months ago
• theislab / troutpy
  Package for the analysis of Transcripts outside segmented cells in ST data
  ☆24Updated this week
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆25Updated last year
• 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
  ☆66Updated 6 months ago
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆33Updated this week
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆82Updated last month
• 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
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆56Updated 6 months ago
• CellProfiling / pipex
  A pipeline to transform images into valuable analysis items
  ☆17Updated 6 months ago
• seqscope / ficture
  ☆42Updated 2 months ago
• ElementoLab / utag
  ☆40Updated last week
• prabhakarlab / Banksy_py
  BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …
  ☆72Updated 2 months ago
• wanglab-broad / CAST
  CAST package
  ☆42Updated last year
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆39Updated last year
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆73Updated this week
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆25Updated 2 months ago
• nf-core / spatialxe
  ☆24Updated last month
• fish-quant / ComSeg
  comseg
  ☆24Updated 11 months ago
• theislab / graphcompass
  GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
  ☆38Updated 6 months ago
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆67Updated last month