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 between single-cell omics data.
☆38Updated 2 years ago
Alternatives and similar repositories for OT-scOmics:
Users that are interested in OT-scOmics are comparing it to the libraries listed below
- Nonnegative spatial factorization for multivariate count data☆57Updated last year
- A simulator for single-cell expression data guided by gene regulatory networks☆58Updated 9 months ago
- Archetypal Analysis network (AAnet)☆31Updated last month
- Alignment of spatial genomics data using deep Gaussian processes☆26Updated 2 years ago
- Regulatory networks with Direct Information in python☆40Updated last year
- Semi-supervised adversarial neural networks for classification of single cell transcriptomics data☆74Updated 2 months ago
- Conditional out-of-distribution prediction☆56Updated 7 months ago
- Quantifying experimental perturbations at single cell resolution☆106Updated 5 months ago
- Gaussian process regression package for counts data with negative binomial and zero-inflated negative binomial likelihoods☆21Updated last week
- Gromov-Wasserstein based optimal transport for aligning single-cell multi-omics data☆68Updated last year
- ☆45Updated 2 years ago
- Dynamical systems methods for RNA velocity analysis☆24Updated 3 years ago
- Template repository for creating novel models with scvi-tools☆19Updated 2 years ago
- Simulate single-cell RNA-SEQ data using the Splatter statistical framework but implemented in python. In addition, simulate doublet cells…☆26Updated 3 years ago
- Git Repo for simulating Boolean Models☆33Updated 8 months ago
- ☆58Updated last year
- ☆98Updated last year
- Global Waddington-OT☆22Updated 6 months ago
- generalized principal component analysis (GLM-PCA) implemented in python☆58Updated 4 years ago
- A collection of scripts and tools for loading, processing, and handling single cell data.☆72Updated last year
- Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Gen…☆40Updated 2 years ago
- A python implementation of scran computeSumFactors: normalization by deconvolution for single-cell RNA-sequencing☆34Updated last year
- Learning cell communication from spatial graphs of cells☆105Updated last year
- MultiMAP for integration of single cell multi-omics☆55Updated last year
- ☆24Updated 5 months ago
- spatial transcriptome, single cell☆67Updated last year
- A quantitative framework for evaluating data structure preservation by dimensionality reduction techniques☆15Updated 3 years ago
- The software of Pamona, a partial manifold alignment algorithm.☆19Updated 3 years ago
- Deep exponential families for single-cell data.☆21Updated 3 months ago
- Reproducing the experiments of the paper "Deep generative modeling for single-cell transcriptomics"☆56Updated 6 years ago