Alternatives and similar repositories for omnipath

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

• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆71Updated 2 years ago
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆50Updated 10 months ago
• saezlab / corneto
  Unified knowledge-driven network inference from omics data
  ☆87Updated last month
• lilab-bcb / harmony-pytorch
  ☆58Updated 6 months ago
• settylab / Mellon
  Non-parametric density inference for single-cell analysis.
  ☆73Updated 6 months ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆114Updated last week
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆102Updated last month
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆62Updated 3 months ago
• Teichlab / MultiMAP
  MultiMAP for integration of single cell multi-omics
  ☆55Updated 2 years ago
• zcang / SpaOTsc
  ☆45Updated 4 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆76Updated 9 months ago
• const-ae / pyLemur
  A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
  ☆28Updated 11 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last month
• mossjacob / pyslingshot
  Python implementation of the Slingshot pseudotime algorithm
  ☆66Updated last month
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆50Updated 7 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆123Updated last week
• KrishnaswamyLab / MELD
  Quantifying experimental perturbations at single cell resolution
  ☆112Updated last year
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆35Updated 2 months ago
• bioFAM / mofapy2
  Multi-omics factor analysis v2
  ☆54Updated last month
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆95Updated last year
• scverse / pytometry
  Flow & mass cytometry analytics.
  ☆57Updated last week
• MarioniLab / sagenet
  Spatial reconstruction of dissociated single-cell data
  ☆19Updated last year
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆44Updated 2 years ago
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆54Updated last year
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆66Updated 4 months ago
• berenslab / umi-normalization
  Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Gen…
  ☆40Updated 3 years ago
• theislab / scTab
  ☆61Updated last year
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆31Updated 2 years ago
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆29Updated last week
• prabhakarlab / Banksy_py
  BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …
  ☆69Updated 3 weeks ago