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
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆61Updated 2 months ago
• const-ae / pyLemur
  A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
  ☆26Updated 9 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆44Updated 3 weeks ago
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 2 weeks ago
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆31Updated 2 weeks ago
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆35Updated 3 weeks ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆42Updated 5 months ago
• gerstung-lab / BaSISS
  Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
  ☆27Updated 2 years ago
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆31Updated 2 years ago
• jkobject / scDataLoader
  a dataloader to work with large single cell datasets from lamindb
  ☆29Updated last week
• wanglab-broad / CAST
  CAST package
  ☆40Updated 11 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆84Updated 3 months ago
• loosolab / scanpro
  A modular tool for proportion analysis in single-cell sequencing data
  ☆23Updated last month
• rajewsky-lab / spacemake
  ☆45Updated 2 weeks ago
• DendrouLab / panpipes
  Multi-modal single cell analysis pipelines
  ☆59Updated this week
• almaan / eggplant
  ☆22Updated 3 years ago
• quadbio / cell-annotator
  Automatically annotate cell types, consistently across samples.
  ☆16Updated 2 months ago
• Teichlab / sctk
  ☆41Updated 2 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
  ☆55Updated last year
• saketkc / pySCTransform
  Python package to perform normalization and variance-stabilization of single-cell data
  ☆25Updated 3 months ago
• Teichlab / snp2cell
  cell type specific, trait-associated gene regulation
  ☆29Updated 6 months ago
• WangPeng-Lab / scGCO
  Single-cell Graph Cuts Optimization
  ☆16Updated last year
• rs239 / velorama
  Gene regulatory network inference for RNA velocity and pseudotime data
  ☆27Updated last month
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆15Updated 2 years ago
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆16Updated last month
• secrierlab / SpottedPy
  Hotspot cluster distance analysis in spatial transcriptomic data
  ☆33Updated 8 months ago
• settylab / Mellon
  Non-parametric density inference for single-cell analysis.
  ☆72Updated 5 months ago
• MICS-Lab / scyan
  Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effe…
  ☆37Updated 11 months ago
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆98Updated 4 months ago