Alternatives and similar repositories for omnipath

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

• saezlab / corneto
  Unified knowledge-driven network inference from omics data
  ☆91Updated 3 weeks ago
• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆73Updated 2 years ago
• lilab-bcb / harmony-pytorch
  ☆62Updated 8 months ago
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆52Updated last year
• bioFAM / mofapy2
  Multi-omics factor analysis v2
  ☆56Updated last week
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆105Updated this week
• const-ae / pyLemur
  A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
  ☆27Updated last year
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆95Updated last year
• KrishnaswamyLab / MELD
  Quantifying experimental perturbations at single cell resolution
  ☆112Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆69Updated 3 months ago
• Teichlab / MultiMAP
  MultiMAP for integration of single cell multi-omics
  ☆55Updated 2 years ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆126Updated 2 months ago
• settylab / Mellon
  Non-parametric density inference for single-cell analysis.
  ☆73Updated 8 months ago
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆31Updated this week
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆34Updated 10 months ago
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆65Updated last week
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆53Updated 9 months ago
• SONGDONGYUAN1994 / scDesign3
  scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
  ☆113Updated 4 months ago
• KrishnaswamyLab / scprep
  A collection of scripts and tools for loading, processing, and handling single cell data.
  ☆76Updated 4 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆81Updated 11 months ago
• shmohammadi86 / ACTIONet
  ACTIONet single-cell analysis framework
  ☆44Updated last year
• MarioniLab / sagenet
  Spatial reconstruction of dissociated single-cell data
  ☆19Updated 2 years ago
• theislab / prophet
  ☆38Updated last month
• mossjacob / pyslingshot
  Python implementation of the Slingshot pseudotime algorithm
  ☆69Updated 3 months ago
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆53Updated last year
• scverse / pytometry
  Flow & mass cytometry analytics.
  ☆58Updated last week
• Teichlab / bbknn
  Batch balanced KNN
  ☆177Updated 2 years ago
• bedapub / besca
  BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis
  ☆50Updated 8 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆62Updated last week
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆116Updated last year