Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
☆67Jul 8, 2025Updated 8 months ago
Alternatives and similar repositories for MIRA
Users that are interested in MIRA are comparing it to the libraries listed below
Sorting:
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆66Feb 11, 2026Updated 3 weeks ago
- Single-cell Transcriptome and Regulome Analysis Pipeline☆303Mar 6, 2023Updated 3 years ago
- Context specific and dynamic gene regulatory network reconstruction and analysis☆127Nov 24, 2025Updated 3 months ago
- Multi-omic velocity inference☆116Oct 23, 2024Updated last year
- Aligning gene expression trajectories of single-cell reference and query systems☆83Aug 10, 2025Updated 6 months ago
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆205Feb 4, 2026Updated last month
- All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs☆41Mar 20, 2023Updated 2 years ago
- trajectory inference☆107Jan 27, 2025Updated last year
- SIMBA: SIngle-cell eMBedding Along with features☆66Oct 16, 2024Updated last year
- 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
- Molecular interactions inference from single-cell multi-omics data☆30Jan 14, 2026Updated last month
- ☆16Feb 11, 2024Updated 2 years ago
- Snakefile-based process to turn 1.4 million ocular cells into a unified meta-atlas☆26Jan 14, 2024Updated 2 years ago
- Reworked clustering metrics for assessing performance in imbalanced settings☆18Jun 3, 2024Updated last year
- 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
- ☆131Nov 17, 2023Updated 2 years ago
- R package IReNA☆29Nov 13, 2024Updated last year
- 𝒫robabilistic modeling of RNA velocity ⬱☆49Feb 16, 2026Updated 2 weeks ago
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Feb 19, 2026Updated 2 weeks ago
- R toolkit for the analysis of single-cell chromatin data☆407Jan 20, 2026Updated last month
- Statistical analysis for spatial omics data☆11Jul 30, 2022Updated 3 years ago
- Reproducibility for the "Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models" paper☆13Jul 15, 2022Updated 3 years ago
- CellRank: dynamics from multi-view single-cell data☆431Updated this week
- Template repository for creating novel models with scvi-tools☆20Jan 18, 2023Updated 3 years ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆179Mar 27, 2025Updated 11 months ago
- muon is a multimodal omics Python framework☆262Jan 19, 2026Updated last month
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆100Sep 9, 2025Updated 5 months ago
- epigenome analysis to rank transcription factors☆32Feb 2, 2023Updated 3 years ago
- A python package for learning mutational signatures and their multidimensional genomic properties☆15Sep 1, 2020Updated 5 years ago
- Camiel's scATAC-seq analysis pipeline☆13Apr 15, 2024Updated last year
- Reproducibility Repo for mvTCR paper☆13Apr 2, 2024Updated last year
- ☆12Nov 20, 2023Updated 2 years ago
- Custom codes accompanying single cell spatial transcriptomic study on the healthy human lung☆13Dec 27, 2023Updated 2 years ago
- ☆13Feb 12, 2026Updated 3 weeks ago
- Analysis Pipeline for Single Cell ATAC-seq☆321Apr 27, 2023Updated 2 years ago
- SCRIP(Single Cell Regulatory network Inference using ChIP-seq) is a tool for evaluating the binding enrichment of specific TR at single-c…☆20Jul 2, 2024Updated last year
- ☆126Jan 31, 2026Updated last month
- Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effe…☆42Nov 22, 2024Updated last year
- Deciphering driver regulators of cell fate decisions from single-cell RNA-seq data☆29Oct 24, 2024Updated last year