Alternatives and similar repositories for Circe:

Users that are interested in Circe are comparing it to the libraries listed below

• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆36Updated last month
• theislab / regvelo
  inferring regulatory cellular dynamics
  ☆34Updated last month
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆60Updated 9 months ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆49Updated 3 weeks ago
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 2 years ago
• HYsxe / PRINT
  ☆36Updated 5 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆36Updated 5 months ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated this week
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆22Updated 3 months ago
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆66Updated last year
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆59Updated last month
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆52Updated 10 months ago
• kunwang34 / PhyloVelo
  PhyloVelo, Phylogeny-based transcriptomic velocity of single cells
  ☆42Updated last year
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆40Updated 7 months ago
• xiaoyeye / TFvelo
  ☆44Updated 9 months ago
• snehamitra / SCARlink
  ☆49Updated 5 months ago
• caleblareau / mtscATACpaper_reproducibility
  Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020
  ☆16Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆62Updated this week
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆28Updated 2 months ago
• mvinyard / ArchR-h5ad
  Parse ArchR arrow files to anndata h5ad
  ☆14Updated last year
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆27Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 8 months ago
• brianpenghe / python-genomics
  A set of files to do genomics analysis on python
  ☆18Updated 2 months ago
• rs239 / velorama
  Gene regulatory network inference for RNA velocity and pseudotime data
  ☆22Updated this week
• andreariba / DeepCycle
  Cell cycle inference in single-cell RNA-seq
  ☆42Updated last year
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆41Updated last year
• AllonKleinLab / cospar
  ☆26Updated last year
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆70Updated 9 months ago
• UPSUTER / GEMLI
  ☆29Updated 3 weeks ago
• multitalk / awesome-cell-cell-communication
  Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
  ☆34Updated last month