Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
☆68Jul 8, 2025Updated 10 months ago
Alternatives and similar repositories for MIRA
Users that are interested in MIRA are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Multi-omic velocity inference☆118Oct 23, 2024Updated last year
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆67Mar 31, 2026Updated last month
- ☆16Feb 11, 2024Updated 2 years ago
- Single-cell Transcriptome and Regulome Analysis Pipeline☆310Mar 6, 2023Updated 3 years ago
- All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs☆41Mar 20, 2023Updated 3 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Context specific and dynamic gene regulatory network reconstruction and analysis☆128Apr 14, 2026Updated 3 weeks ago
- Aligning gene expression trajectories of single-cell reference and query systems☆88Aug 10, 2025Updated 8 months ago
- trajectory inference☆109Jan 27, 2025Updated last year
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆215Feb 4, 2026Updated 3 months ago
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Feb 19, 2026Updated 2 months ago
- 𝒫robabilistic modeling of RNA velocity ⬱☆49Apr 30, 2026Updated last week
- R package IReNA☆30Nov 13, 2024Updated last year
- SIMBA: SIngle-cell eMBedding Along with features☆66Oct 16, 2024Updated last year
- Reproducibility for the "Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models" paper☆13Jul 15, 2022Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- 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
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆251Jan 16, 2026Updated 3 months ago
- R toolkit for the analysis of single-cell chromatin data☆415Apr 20, 2026Updated 2 weeks ago
- Analysis of imbalanced data and its impacts in a scRNA-seq integration setting☆31Mar 7, 2025Updated last year
- epigenome analysis to rank transcription factors☆33Feb 2, 2023Updated 3 years ago
- Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.☆31May 27, 2025Updated 11 months ago
- Template repository for creating novel models with scvi-tools☆20Jan 18, 2023Updated 3 years ago
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆102Sep 9, 2025Updated 7 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- 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
- Reproducibility Repo for mvTCR paper☆13Apr 2, 2024Updated 2 years ago
- Analysis Pipeline for Single Cell ATAC-seq☆322Apr 27, 2023Updated 3 years ago
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆122Jan 22, 2024Updated 2 years ago
- Deciphering driver regulators of cell fate decisions from single-cell RNA-seq data☆30Oct 24, 2024Updated last year
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆187Mar 27, 2025Updated last year
- ☆132Nov 17, 2023Updated 2 years ago
- CellRank: dynamics from multi-view single-cell data☆443Updated this week
- A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data☆82Jul 25, 2025Updated 9 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆33Nov 9, 2022Updated 3 years ago
- ☆127Mar 19, 2026Updated last month
- cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data☆147Apr 5, 2024Updated 2 years ago
- SCRAT: Single-Cell Regulome Analysis Tool☆16Apr 4, 2020Updated 6 years ago
- Pipeline for designing custom probes against human genes☆22Jan 30, 2026Updated 3 months ago
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆58Jan 29, 2026Updated 3 months ago
- muon is a multimodal omics Python framework☆266Mar 16, 2026Updated last month