gifford-lab / prescient
Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
☆45Updated last month
Alternatives and similar repositories for prescient:
Users that are interested in prescient are comparing it to the libraries listed below
- Python implementation of Milo for differential abundance testing on KNN graph☆62Updated this week
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆52Updated 6 months ago
- Quasilinear data representations for single-cell omics data analysis☆42Updated last year
- Single cell omics biology annotations☆49Updated 3 weeks ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆59Updated 8 months ago
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆60Updated 9 months ago
- Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data☆24Updated 2 years ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆36Updated 5 months ago
- Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…☆47Updated 2 weeks ago
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 2 years ago
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆109Updated last year
- Multi-resolution Variational Inference☆22Updated this week
- Geometry-preserving random sampling☆78Updated 3 months ago
- ☆26Updated last year
- cTPnet Package☆24Updated 2 years ago
- ☆51Updated last year
- This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.☆31Updated 7 months ago
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆39Updated 3 years ago
- ☆45Updated 2 years ago
- An interpretable simulator that generates realistic single-cell gene expression count data with gene correlations recapitulated☆24Updated 3 months ago
- PhyloVelo, Phylogeny-based transcriptomic velocity of single cells☆42Updated last year
- Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).☆19Updated last week
- ACTIONet single-cell analysis framework☆38Updated 5 months ago
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆50Updated last month
- ☆47Updated last year
- UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference☆26Updated 3 months ago
- Code for Universal Single-Cell Matching with Unpaired Feature Sets☆21Updated 3 years ago
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆23Updated 6 months ago
- A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.☆24Updated last month
- Spatial direct messaging detected by bivariate Moran☆25Updated last month