Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
☆189Jan 30, 2026Updated last month
Alternatives and similar repositories for spectra
Users that are interested in spectra are comparing it to the libraries listed below
Sorting:
- Single cell omics biology annotations☆54Apr 20, 2025Updated 10 months ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆179Mar 27, 2025Updated 11 months ago
- ☆62Dec 8, 2025Updated 2 months ago
- Context specific and dynamic gene regulatory network reconstruction and analysis☆127Nov 24, 2025Updated 3 months ago
- Gene group activity utility functions for Scanpy☆100Dec 21, 2024Updated last year
- R package for pathway analysis in scRNA-seq data☆77Aug 17, 2024Updated last year
- Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition☆64Apr 14, 2024Updated last year
- Code for scKINETICS (ISMB 2023)☆22Oct 23, 2023Updated 2 years ago
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆66Feb 11, 2026Updated 2 weeks ago
- LIANA: a LIgand-receptor ANalysis frAmework☆232Aug 7, 2024Updated last year
- ☆52Oct 9, 2025Updated 4 months ago
- Reference mapping for single-cell genomics☆399Dec 2, 2025Updated 2 months ago
- CellRank: dynamics from multi-view single-cell data☆430Updated this week
- Multi-modal single cell analysis pipelines☆62Dec 11, 2025Updated 2 months ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆420Sep 4, 2025Updated 5 months ago
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆118Jan 22, 2024Updated 2 years ago
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆247Jan 16, 2026Updated last month
- A single-cell analysis toolkit to jointly analyze samples from distinct conditions☆34Apr 2, 2025Updated 10 months ago
- Metacells - Single-cell RNA Sequencing Analysis☆120Sep 27, 2024Updated last year
- A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data☆79Jul 25, 2025Updated 7 months ago
- single cell Flux Estimation Analysis (scFEA) Try the below web server!☆143Nov 10, 2023Updated 2 years ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆378Jul 30, 2025Updated 7 months ago
- Analysis of cell-cell communication at single-cell resolution☆106Sep 10, 2024Updated last year
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆138Feb 20, 2025Updated last year
- LIANA+: an all-in-one framework for cell-cell communication☆271Jan 24, 2026Updated last month
- This is the alpha version of the CellOracle package☆421Feb 3, 2026Updated 3 weeks ago
- Bayesian mixed-effect model to test differences in cell type proportions from single-cell data, in R☆120Updated this week
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆76Nov 2, 2025Updated 3 months ago
- In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes☆121Oct 31, 2025Updated 4 months ago
- A tool for semi-automatic cell type classification☆453Updated this week
- Learning meaningful representations of genes☆21Jul 7, 2025Updated 7 months ago
- Aligning gene expression trajectories of single-cell reference and query systems☆83Aug 10, 2025Updated 6 months ago
- Multi-omic velocity inference☆116Oct 23, 2024Updated last year
- A package to help convert different single-cell data formats to each other☆458Feb 20, 2026Updated last week
- R package for semi-supervised single-cell data integration☆96Jan 27, 2026Updated last month
- The first computational tool that enables both unsupervised and supervised discovery of tissue spatial domains☆34Apr 11, 2025Updated 10 months ago
- Single-cell perturbation analysis☆289Updated this week
- Querying cellular states and programs by learning representations of gene sets☆16Nov 2, 2025Updated 3 months ago
- ☆60Apr 5, 2024Updated last year