Alternatives and similar repositories for topometry:

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

• pachterlab / picasso
  Picasso: a methods for embedding points in 2D in a way that respects distances while fitting a user-specified shape.
  ☆70Updated 9 months ago
• willtownes / glmpca-py
  generalized principal component analysis (GLM-PCA) implemented in python
  ☆60Updated 4 years ago
• dawe / schist
  An interface for Nested Stochastic Block Model for single cell analysis
  ☆32Updated last month
• cantinilab / OT-scOmics
  This Python package will allow you to replicate the experiments from our research on applying Optimal Transport as a similarity metric in…
  ☆38Updated 2 years ago
• cantinilab / Mowgli
  Single-cell multi-omics integration using Optimal Transport
  ☆43Updated 7 months ago
• KrishnaswamyLab / scprep
  A collection of scripts and tools for loading, processing, and handling single cell data.
  ☆72Updated last year
• czbiohub-sf / simscity
  A library to simulate single-cell data
  ☆2Updated 2 years ago
• pachterlab / MCML
  ☆33Updated 3 years ago
• quadbio / latent-lego
  Latent spaces for single cells
  ☆21Updated last year
• aristoteleo / Scribe-py
  Regulatory networks with Direct Information in python
  ☆40Updated 2 years ago
• rongstat / meta-visualization
  A spectral method for assessing and combining multiple data visualizations
  ☆49Updated last year
• davisidarta / dbMAP
  A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions…
  ☆48Updated 4 years ago
• calico / velodyn
  Dynamical systems methods for RNA velocity analysis
  ☆24Updated 3 years ago
• KrishnaswamyLab / MELD
  Quantifying experimental perturbations at single cell resolution
  ☆106Updated 7 months ago
• Teichlab / MultiMAP
  MultiMAP for integration of single cell multi-omics
  ☆56Updated last year
• RabadanLab / scTDA
  An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data
  ☆7Updated 7 years ago
• CamaraLab / scTDA
  An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data
  ☆51Updated 6 years ago
• KrishnaswamyLab / Multiscale_PHATE
  Creating multi-resolution embeddings and clusters from high dimensional data
  ☆53Updated 7 months ago
• krassowski / gsea-api
  Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)
  ☆14Updated 2 years ago
• cbg-ethz / scDEF
  Deep exponential families for single-cell data.
  ☆21Updated 5 months ago
• theislab / batchglm
  Fit generalized linear models in python.
  ☆27Updated 2 years ago
• ismms-himc / visium-clustergrammer2
  Spatial Transcriptomics Dashboard
  ☆28Updated last year
• pinellolab / pyrovelocity
  𝒫robabilistic modeling of RNA velocity ⬱
  ☆47Updated this week
• fanzheng10 / HiDeF
  HiDeF (Hierarchical community Decoding Framework)
  ☆14Updated 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
• KrishnaswamyLab / graphtools
  Tools for building and manipulating graphs in Python
  ☆41Updated 2 years ago
• shwhalen / ml-pitfalls
  Notebooks accompanying the paper "Navigating the pitfalls of applying machine learning in genomics"
  ☆45Updated last year
• scverse / conference-2024
  Slides and Notebooks for scverse 2024
  ☆17Updated 7 months ago
• simslab / scHPF
  Single-cell Hierarchical Poisson Factorization
  ☆69Updated 2 years ago
• saezlab / omnipath
  Python client for the OmniPath web service
  ☆44Updated last month