R package for analysing single cell data
☆64Dec 8, 2022Updated 3 years ago
Alternatives and similar repositories for speckle
Users that are interested in speckle are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- R package for specialised analysis of single cell data☆41Oct 14, 2022Updated 3 years ago
- Single-cell analysis with non-negative matrix factorization☆48Jul 24, 2025Updated 8 months ago
- CellAnn☆12Nov 3, 2023Updated 2 years ago
- marker-based purification of cell types from single-cell RNA-seq datasets☆141Mar 13, 2026Updated last month
- Significance analysis for clustering single-cell RNA-sequencing data☆123Sep 7, 2024Updated last year
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis☆23Oct 25, 2024Updated last year
- Single-cell immune repertoire trajectory analysis in R☆12Aug 8, 2025Updated 8 months ago
- High dimensional weighted gene co-expression network analysis☆469Mar 13, 2026Updated last month
- Coarse-graining of large single-cell RNA-seq data into metacells☆99Feb 23, 2026Updated last month
- This repository contained single-cell RNA-seq datasets with ICB treated patients☆15Nov 8, 2024Updated last year
- R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆295Updated this week
- Wrapper and helper functions to use bulk RNA-seq differential expression methods with single-cell data☆21Feb 4, 2024Updated 2 years ago
- Flexible Integration of single-cell RNA-sequencing data for large-scale Multi-tissue cell atlas datasets☆13Sep 20, 2022Updated 3 years ago
- R package developed for single-cell RNA-seq analysis. It was designed using the Seurat framework, and offers existing and novel single-ce…☆33Nov 28, 2025Updated 4 months ago
- Serverless GPU API endpoints on Runpod - Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- ☆27Jun 5, 2025Updated 10 months ago
- code and files for SPARC curation workflows☆17Mar 24, 2026Updated 3 weeks ago
- ☆12Nov 7, 2022Updated 3 years ago
- Multi-sample multi-group scRNA-seq analysis tools☆223Mar 25, 2026Updated 2 weeks ago
- R package for detection of cell-cell interaction using Non-negative Tensor Decomposition☆35Jun 19, 2025Updated 9 months ago
- ☆14May 7, 2022Updated 3 years ago
- Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.☆94Dec 18, 2024Updated last year
- an integrative analysis tool for analysing large-scale single cell RNA-sequencing data☆36Aug 7, 2023Updated 2 years ago
- A database of useful gene signatures for single-cell analysis☆28May 19, 2025Updated 10 months ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Bayesian mixed-effect model to test differences in cell type proportions from single-cell data, in R☆123Updated this week
- Code to run the scHLApers pipeline for personalized single-cell HLA quantification☆17Jan 10, 2024Updated 2 years ago
- General notes and resources on how to analyze Spatial Transcriptomics data☆12Jun 20, 2023Updated 2 years ago
- Single-cell analytic toolbox that offers modular workflows for multi-level cellular annotation and user-friendly analysis reports☆11Mar 31, 2026Updated 2 weeks ago
- Calibrated clustering with artificial variables to avoid over-clustering in single-cell RNA-sequencing☆19Nov 18, 2025Updated 4 months ago
- Interactively analyze single cell genomic data☆186Jan 14, 2026Updated 3 months ago
- ☆58Jan 2, 2024Updated 2 years ago
- AWS for Bioinformatics Researchers☆188Jul 17, 2025Updated 8 months ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆425Updated this week
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- LIANA: a LIgand-receptor ANalysis frAmework☆238Aug 7, 2024Updated last year
- Easy single cell analysis platform for enrichment☆218Apr 3, 2026Updated last week
- Gene set scoring for single-cell data☆189Feb 11, 2026Updated 2 months ago
- A post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping☆28Apr 5, 2026Updated last week
- scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics☆117Sep 29, 2025Updated 6 months ago
- sharing interactive single cell gene expression visualizations from Seurat☆12May 18, 2023Updated 2 years ago
- R package for pathway analysis in scRNA-seq data☆79Aug 17, 2024Updated last year