Alternatives and similar repositories for cookiecutter-scverse

Users that are interested in cookiecutter-scverse are comparing it to the libraries listed below

• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆99Updated last month
• scverse / pytometry
  Flow & mass cytometry analytics.
  ☆53Updated last week
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆62Updated last week
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆80Updated 3 weeks ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆105Updated this week
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 5 months ago
• theislab / moscot
  Multi-omic single-cell optimal transport tools
  ☆165Updated this week
• scverse / ecosystem-packages
  Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
  ☆25Updated this week
• lilab-bcb / harmony-pytorch
  ☆55Updated last month
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆38Updated last week
• scverse / pertpy
  Perturbation Analysis in the scverse ecosystem.
  ☆186Updated this week
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆50Updated last year
• saketkc / pySCTransform
  Python package to perform normalization and variance-stabilization of single-cell data
  ☆24Updated 3 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…
  ☆36Updated 7 months ago
• scverse / scvi-tools-skeleton
  Template repository for creating novel models with scvi-tools
  ☆20Updated 2 years ago
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆212Updated last week
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆100Updated 3 months ago
• atarashansky / SCTransformPy
  A python port of the R package SCTransform:
  ☆20Updated 4 years ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆144Updated 7 months ago
• openproblems-bio / openproblems-v2
  Formalizing and benchmarking open problems in single-cell genomics
  ☆56Updated last month
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆72Updated last month
• YosefLab / Cassiopeia
  A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
  ☆90Updated last week
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆57Updated last month
• chanzuckerberg / single-cell-curation
  Code and documentation for the curation of cellxgene datasets
  ☆47Updated this week
• jkobject / scPRINT
  single cell foundation model for Gene network inference and more
  ☆17Updated 3 weeks ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆137Updated last week
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆28Updated 2 years ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆165Updated last year
• scverse / muon
  muon is a multimodal omics Python framework
  ☆239Updated 4 months ago
• theislab / graphcompass
  GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
  ☆36Updated this week