Alternatives and similar repositories for ecosystem-packages

Users that are interested in ecosystem-packages are comparing it to the libraries listed below

• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆43Updated last week
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆60Updated last month
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆83Updated last month
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 8 months ago
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆33Updated last month
• wanglab-broad / CAST
  CAST package
  ☆40Updated 10 months ago
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆38Updated last week
• const-ae / pyLemur
  A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
  ☆26Updated 8 months ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆24Updated last year
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆64Updated 2 months ago
• scverse / genomic-features
  Genomic Features in Python from BioConductor's AnnotationHub
  ☆22Updated this week
• scverse / conference-2024
  Slides and Notebooks for scverse 2024
  ☆17Updated 11 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆64Updated last week
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆99Updated 3 months ago
• gerstung-lab / BaSISS
  Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
  ☆26Updated 2 years ago
• sagar87 / spatialproteomics
  Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…
  ☆33Updated this week
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆29Updated this week
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆38Updated 6 months ago
• lilab-bcb / harmony-pytorch
  ☆55Updated 3 months ago
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆31Updated 2 weeks ago
• scverse / spatialdata-io
  ☆68Updated this week
• damienArnol / svca
  ☆13Updated 6 years ago
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆16Updated 4 months ago
• loosolab / scanpro
  A modular tool for proportion analysis in single-cell sequencing data
  ☆23Updated this week
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆27Updated last month
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆55Updated last week
• saketkc / pySCTransform
  Python package to perform normalization and variance-stabilization of single-cell data
  ☆24Updated last month
• jkobject / scDataLoader
  a dataloader to work with large single cell datasets from lamindb
  ☆29Updated last week
• Sanofi-Public / spatialone-pipeline
  Spatial One
  ☆28Updated 10 months ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆109Updated last week