Alternatives and similar repositories for bento-tools

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

• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆48Updated 2 months ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆108Updated last month
• scverse / spatialdata-notebooks
  ☆65Updated last week
• scverse / spatialdata-io
  ☆88Updated last week
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆51Updated this week
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆45Updated 7 months ago
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆105Updated last week
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆66Updated 7 months ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆95Updated 2 years ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆25Updated last year
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆65Updated 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…
  ☆39Updated this week
• ElementoLab / utag
  ☆41Updated last week
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆84Updated 2 weeks ago
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆25Updated 3 months ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆56Updated 7 months ago
• 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 / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆33Updated last week
• 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
  ☆75Updated 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
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• wanglab-broad / CAST
  CAST package
  ☆42Updated last year
• theislab / troutpy
  Package for the analysis of Transcripts outside segmented cells in ST data
  ☆25Updated this week
• Feanor007 / MESA
  A python package for Multiomics and Ecological Spatial Analysis (MESA)
  ☆23Updated 9 months ago
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆15Updated 2 years ago
• theislab / multimil
  Weakly supervised learning uncovers phenotypic signatures in single-cell data
  ☆38Updated last month
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆107Updated this week
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆42Updated 11 months ago
• CellProfiling / pipex
  A pipeline to transform images into valuable analysis items
  ☆18Updated 7 months ago