Alternatives and similar repositories for PHATE

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

• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆423Updated this week
• KrishnaswamyLab / MAGIC
  MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …
  ☆360Updated 7 months ago
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆215Updated 4 years ago
• berenslab / rna-seq-tsne
  The art of using t-SNE for single-cell transcriptomics
  ☆123Updated 5 months ago
• facebookresearch / PoincareMaps
  The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRN…
  ☆148Updated 3 years ago
• kipoi / kipoi
  Kipoi's model zoo API
  ☆236Updated last year
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆449Updated 4 months ago
• openproblems-bio / openproblems
  Formalizing and benchmarking open problems in single-cell genomics
  ☆332Updated 3 weeks ago
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆217Updated 10 months ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆438Updated 2 months ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆381Updated last month
• ponnhide / pyCircos
  python Circos
  ☆356Updated 10 months ago
• reneshbedre / bioinfokit
  Bioinformatics data analysis and visualization toolkit
  ☆350Updated 11 months ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆348Updated 3 months ago
• mortazavilab / PyWGCNA
  PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
  ☆243Updated 2 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆363Updated 2 months ago
• broadinstitute / wot
  A software package for analyzing snapshots of developmental processes
  ☆146Updated 2 years ago
• scverse / anndata
  Annotated data.
  ☆621Updated this week
• bioFAM / MOFA2
  Multi-Omics Factor Analysis
  ☆329Updated 10 months ago
• jacoblevine / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆138Updated 4 years ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆334Updated 2 months ago
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆289Updated 2 months ago
• hhcho / densvis
  Density-preserving data visualization tools den-SNE and densMAP
  ☆111Updated 4 years ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆500Updated last year
• pachterlab / BI-BE-CS-183-2023
  Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023
  ☆480Updated last year
• kundajelab / tfmodisco
  TF MOtif Discovery from Importance SCOres
  ☆136Updated last year
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆626Updated last month
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆698Updated 3 weeks ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆235Updated 2 months ago
• FunctionLab / selene
  a framework for training sequence-level deep learning networks
  ☆381Updated 4 months ago