Alternatives and similar repositories for liana-py

Users that are interested in liana-py are comparing it to the libraries listed below

• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆241Updated this week
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆239Updated 10 months ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆180Updated last week
• scverse / pertpy
  Single-cell perturbation analysis
  ☆217Updated last week
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆224Updated last year
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆226Updated last year
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆415Updated 4 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆167Updated 3 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆229Updated this week
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆169Updated 8 months ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆431Updated last week
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆180Updated last year
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆198Updated last week
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆393Updated this week
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆145Updated 2 years ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆300Updated 3 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆183Updated 2 years ago
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆301Updated last week
• scverse / rapids_singlecell
  rapids_singlecell: GPU-accelerated framework for scRNA analysis
  ☆279Updated this week
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆205Updated last month
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆227Updated 5 months ago
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆235Updated last month
• digitalcytometry / cytotrace2
  CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.
  ☆199Updated last month
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆161Updated 4 years ago
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆193Updated last week
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆149Updated last year
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆168Updated 2 years ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆394Updated 3 weeks ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆257Updated 3 weeks ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆150Updated 4 months ago