Alternatives and similar repositories for ecosystem-packages

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

• scverse / genomic-features
  Genomic Features in Python from BioConductor's AnnotationHub
  ☆22Updated this week
• const-ae / pyLemur
  A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
  ☆28Updated 10 months ago
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆32Updated last month
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆61Updated 3 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆45Updated last week
• gerstung-lab / BaSISS
  Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
  ☆27Updated 2 years ago
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated last month
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆16Updated last month
• loosolab / scanpro
  A modular tool for proportion analysis in single-cell sequencing data
  ☆23Updated last month
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆31Updated 2 years ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆83Updated 2 weeks ago
• DendrouLab / panpipes
  Multi-modal single cell analysis pipelines
  ☆59Updated 3 weeks ago
• jkobject / scDataLoader
  a dataloader to work with large single cell datasets from lamindb
  ☆29Updated last week
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆35Updated last month
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆33Updated last week
• wanglab-broad / CAST
  CAST package
  ☆40Updated last year
• almaan / eggplant
  ☆22Updated 3 years ago
• scverse / conference-2024
  Slides and Notebooks for scverse 2024
  ☆17Updated last year
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆98Updated 2 weeks ago
• lilab-bcb / harmony-pytorch
  ☆57Updated 5 months ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆43Updated 5 months ago
• rajewsky-lab / spacemake
  ☆45Updated last week
• settylab / Mellon
  Non-parametric density inference for single-cell analysis.
  ☆72Updated 5 months ago
• azizilab / decipher
  A single-cell analysis toolkit to jointly analyze samples from distinct conditions
  ☆34Updated 7 months ago
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆56Updated last year
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated this week
• Teichlab / sctk
  ☆43Updated last week
• sagar87 / spatialproteomics
  Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…
  ☆38Updated last week
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last week
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆30Updated last year