Alternatives and similar repositories for omnipath:

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

• brianhie / geosketch
  Geometry-preserving random sampling
  ☆78Updated 3 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆62Updated last year
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆48Updated this week
• dpeerlab / scKINETICS
  Code for scKINETICS (ISMB 2023)
  ☆21Updated last year
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆44Updated last week
• lilab-bcb / harmony-pytorch
  ☆50Updated last year
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆82Updated last week
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆47Updated 6 months ago
• saezlab / corneto
  Unified knowledge-driven network inference from omics data
  ☆30Updated last week
• LungCellAtlas / mapping_data_to_the_HLCA
  Repository to perform mapping of new datasets to the Human Lung Cell Atlas.
  ☆19Updated last year
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆22Updated 2 months ago
• Teichlab / MultiMAP
  MultiMAP for integration of single cell multi-omics
  ☆54Updated last year
• settylab / Mellon
  Non-parametric density inference for single-cell analysis.
  ☆65Updated last month
• theislab / pseudodynamics
  Dynamic models for single-cell RNA-seq time series.
  ☆39Updated 6 years ago
• cellatlas / human
  ☆42Updated 3 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆108Updated 3 months ago
• zcang / SpaOTsc
  ☆45Updated 2 years ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆60Updated 9 months 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 5 months ago
• DendrouLab / panpipes
  Multi-modal single cell analysis pipelines
  ☆58Updated this week
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆36Updated 4 months ago
• decomverse / ACTIONet
  ACTIONet single-cell analysis framework
  ☆37Updated 4 months ago
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆27Updated last year
• berenslab / umi-normalization
  Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Gen…
  ☆40Updated 2 years ago
• aristoteleo / Scribe-py
  Regulatory networks with Direct Information in python
  ☆39Updated last year
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆91Updated this week
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 7 months ago
• chanzuckerberg / single-cell-curation
  Code and documentation for the curation of cellxgene datasets
  ☆39Updated this week
• theislab / prophet
  ☆27Updated last month
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆97Updated last year