dylkot / scsim
Simulate single-cell RNA-SEQ data using the Splatter statistical framework but implemented in python. In addition, simulate doublet cells and cells with shared gene-expression programs.
☆26Updated 3 years ago
Alternatives and similar repositories for scsim:
Users that are interested in scsim are comparing it to the libraries listed below
- ☆26Updated last year
- A python package for chromVAR☆27Updated last year
- Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.☆44Updated 6 months ago
- Nonnegative spatial factorization for multivariate count data☆57Updated last year
- CAST package☆27Updated 2 months ago
- MARIO: single-cell proteomic data matching and integration using both shared and distinct features☆22Updated last year
- A quantitative framework for evaluating data structure preservation by dimensionality reduction techniques☆15Updated 3 years ago
- Test genes for Spatial Variation☆14Updated 3 weeks ago
- Template repository for creating novel models with scvi-tools☆19Updated 2 years ago
- ☆45Updated 2 years ago
- Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Gen…☆41Updated 2 years ago
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆50Updated last week
- Code for Universal Single-Cell Matching with Unpaired Feature Sets☆20Updated 3 years ago
- ☆43Updated 3 months ago
- Spatial direct messaging detected by bivariate Moran☆24Updated this week
- Regulatory networks with Direct Information in python☆39Updated last year
- Dynamic models for single-cell RNA-seq time series.☆39Updated 6 years ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆36Updated 4 months ago
- Dynamical systems methods for RNA velocity analysis☆24Updated 3 years ago
- Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…☆47Updated 2 months ago
- Learning motif contributions to cell transitions using sequence features and graphs.☆28Updated 4 months ago
- scOpen: single-cell open chromatin analysis via NMF modelling☆25Updated last year
- Python package for integrating and analyzing multiple single-cell datasets (A Python version of LIGER)☆28Updated 6 months ago
- Probabilistic factor models for spatially correlated data. Includes nonnegative and real-valued versions.☆13Updated last month
- PRObabilistic Simulations of ScRNA-seq Tree-like Topologies☆26Updated last year
- Code for scKINETICS (ISMB 2023)☆21Updated last year
- ☆20Updated 2 years ago
- A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.☆19Updated 2 weeks ago
- End-to-end analysis of spatial multi-omics data☆39Updated last week
- Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data☆24Updated 2 years ago