A single-cell analysis toolkit to jointly analyze samples from distinct conditions
☆34Apr 2, 2025Updated 10 months ago
Alternatives and similar repositories for decipher
Users that are interested in decipher are comparing it to the libraries listed below
Sorting:
- ☆13Nov 3, 2023Updated 2 years ago
- Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)☆25Feb 12, 2026Updated 2 weeks ago
- Aligning gene expression trajectories of single-cell reference and query systems☆83Aug 10, 2025Updated 6 months ago
- ☆16Sep 1, 2023Updated 2 years ago
- ☆13Aug 9, 2022Updated 3 years ago
- Code, data and analysis for moslin.☆15Oct 7, 2024Updated last year
- ☆31Jun 10, 2025Updated 8 months ago
- Gene Expression Decomposition and Integration☆19Feb 9, 2026Updated 2 weeks ago
- Pairwise Hierarchical Model☆20Mar 11, 2022Updated 3 years ago
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆41Jan 11, 2025Updated last year
- Non-parametric density inference for single-cell analysis.☆73May 22, 2025Updated 9 months ago
- Analysis of imbalanced data and its impacts in a scRNA-seq integration setting☆31Mar 7, 2025Updated 11 months ago
- Code and example of the D-SPIN framework☆24Jan 12, 2026Updated last month
- ☆36Apr 16, 2025Updated 10 months ago
- Consensus peaks of chromatin accessibility in the human genome☆16Dec 1, 2025Updated 3 months ago
- Single cell omics biology annotations☆54Apr 20, 2025Updated 10 months ago
- single-cell decorrelated module networks☆30Aug 24, 2024Updated last year
- Single-cell perturbation analysis☆289Updated this week
- Querying cellular states and programs by learning representations of gene sets☆16Nov 2, 2025Updated 3 months ago
- R package for gene selection using k-NN graphs.☆13Jun 12, 2023Updated 2 years ago
- Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA☆84Apr 21, 2025Updated 10 months ago
- A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…☆234Jan 2, 2026Updated last month
- Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms☆189Jan 30, 2026Updated last month
- ☆63Sep 13, 2024Updated last year
- scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism☆18Oct 17, 2024Updated last year
- scVI extension for unspliced RNA☆16May 18, 2025Updated 9 months ago
- Single cell STEM (scSTEM) is a shiny app based R package for visualizing and clustering genes in pseudotime ordered single cell RNA-seq d…☆19Jul 7, 2022Updated 3 years ago
- python API to the CoGAPS NMF package☆19May 19, 2025Updated 9 months ago
- Context specific and dynamic gene regulatory network reconstruction and analysis☆127Nov 24, 2025Updated 3 months ago
- Bayesian model for RNA velocity estimation of periodic manifolds☆35Jun 25, 2024Updated last year
- cell type specific, trait-associated gene regulation☆29Mar 31, 2025Updated 11 months ago
- Learning meaningful representations of genes☆21Jul 7, 2025Updated 7 months ago
- ☆17Jul 8, 2024Updated last year
- Vector representations of gene co-expression in single cell RNAseq.☆36Nov 8, 2025Updated 3 months ago
- Scripts from the GBM cellular states paper☆20Feb 24, 2021Updated 5 years ago
- ☆33Jan 23, 2025Updated last year
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆85Mar 20, 2025Updated 11 months ago
- Weakly supervised learning uncovers phenotypic signatures in single-cell data☆38Dec 17, 2025Updated 2 months ago
- A library for the deconvolution of bulk cell samples using single-cell RNA expression data.☆23Nov 3, 2021Updated 4 years ago