openproblems-bio / openproblems-v2Links
Formalizing and benchmarking open problems in single-cell genomics
☆57Updated 6 months ago
Alternatives and similar repositories for openproblems-v2
Users that are interested in openproblems-v2 are comparing it to the libraries listed below
Sorting:
- Unsupervised Deep Disentangled Representation of Single-Cell Omics☆56Updated last week
- Accelerated, Python-only, single-cell integration benchmarking metrics☆79Updated this week
- Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms☆184Updated last year
- scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics☆111Updated 2 months ago
- Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.☆146Updated 2 years ago
- CZ CELLxGENE Discover Census☆114Updated last week
- scPerturb: A resource and a python/R tool for single-cell perturbation data☆156Updated 9 months ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆58Updated this week
- Multi-omic velocity inference☆113Updated last year
- Python implementation of Milo for differential abundance testing on KNN graph☆77Updated 10 months ago
- Additional code and analysis from the single-cell integration benchmarking project☆69Updated 3 years ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆172Updated 8 months ago
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆116Updated last year
- ☆59Updated 7 months ago
- Context specific and dynamic gene regulatory network reconstruction and analysis☆125Updated 3 weeks ago
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆100Updated 3 months ago
- ☆89Updated last year
- Single cell omics biology annotations☆51Updated 8 months ago
- Models and datasets for perturbational single-cell omics☆170Updated 3 years ago
- Geometry-preserving random sampling☆95Updated last year
- Python implementation of the Slingshot pseudotime algorithm☆67Updated last month
- Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.☆29Updated 3 weeks ago
- Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.☆51Updated 11 months ago
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆47Updated 4 years ago
- data and model repository for single-cell data☆136Updated 2 years ago
- single cell foundation model for Gene network inference and more☆18Updated 3 weeks ago
- Clonotype Neighbor Graph Analysis☆93Updated 3 months ago
- End-to-end analysis of spatial multi-omics data☆99Updated last month
- A simulator for single cell multi-omics and spatial omics data that provides ground truth to benchmark a wide range of methods.☆65Updated last month
- A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…☆228Updated 5 months ago