Alternatives and similar repositories for milopy:

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

• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 9 months ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆50Updated last week
• 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
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated 10 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆69Updated 2 months ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆66Updated last week
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆100Updated 6 months ago
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆29Updated last week
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆40Updated 3 years ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆61Updated 6 months ago
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆57Updated 11 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆99Updated last year
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆46Updated 2 months ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆42Updated last year
• cantinilab / Circe
  Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).
  ☆20Updated last month
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆103Updated 5 months ago
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆66Updated last year
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆80Updated 4 months ago
• YosefLab / popV
  ☆71Updated this week
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆61Updated 3 years ago
• HYsxe / PRINT
  ☆36Updated 6 months ago
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆41Updated last year
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆110Updated last year
• lilab-bcb / harmony-pytorch
  ☆51Updated this week
• multitalk / awesome-cell-cell-communication
  Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
  ☆39Updated 2 weeks ago
• data2intelligence / CytoSig
  ☆49Updated 5 months ago
• snehamitra / SCARlink
  ☆50Updated 6 months ago
• zhengrongbin / MEBOCOST
  A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data
  ☆71Updated 4 months ago
• SONGDONGYUAN1994 / scDesign3
  scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
  ☆90Updated 3 weeks 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
  ☆52Updated 7 months ago