A benchmark of batch-effect correction methods for single-cell RNA sequencing data
☆79Jan 24, 2022Updated 4 years ago
Alternatives and similar repositories for Batch-effect-removal-benchmarking
Users that are interested in Batch-effect-removal-benchmarking are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- BERMUDA (Batch Effect ReMoval Using Deep Autoencoders) is a novel transfer-learning-based method for batch correction in scRNA-seq data.☆30Dec 29, 2019Updated 6 years ago
- Code and Data Availability for Single cell transcriptomics reveals a signaling roadmap coordinating endoderm and mesoderm lineage diversi…☆10Apr 16, 2020Updated 6 years ago
- Reproducibility code for the manuscript: 'Inferring and perturbing cell fate regulomes in human cerebral organoids☆31Aug 8, 2023Updated 2 years ago
- An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.☆171Jan 26, 2024Updated 2 years ago
- Analaysis for the batch correction paper☆12Apr 26, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- BEER: Batch EffEct Remover for single-cell data☆25Jan 9, 2025Updated last year
- Evaluation of Cell Type Annotation R Packages on Single Cell RNA-seq Data☆31Feb 20, 2024Updated 2 years ago
- scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks☆10Aug 4, 2020Updated 5 years ago
- single cell sequencing analysis tutorial☆18Jan 15, 2020Updated 6 years ago
- R package for integrating and analyzing multiple single-cell datasets☆429Feb 4, 2026Updated 3 months ago
- A computational method for comparing cellular profiles with the flexibility to place a higher weight on functional features of interest.☆12Jan 31, 2023Updated 3 years ago
- R-code used for single-cell RNA-Seq analysis of kidney data.☆18Oct 17, 2019Updated 6 years ago
- The million-scale method for single-cell analysis☆10Jul 6, 2023Updated 2 years ago
- A novel unsupervised batch removal framework, called iMAP, based on neural networks.☆35Jan 12, 2022Updated 4 years ago
- 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.
- This repository contains HCA Benchmarking codes☆26Nov 11, 2019Updated 6 years ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆643Apr 21, 2026Updated 2 weeks ago
- ☆15Aug 17, 2023Updated 2 years ago
- JEME method for predicting enhancer targets☆11Jul 15, 2017Updated 8 years ago
- Benchmarking analysis of data integration tools☆414Apr 27, 2026Updated last week
- This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset☆153Jan 6, 2021Updated 5 years ago
- Community-provided extensions to Seurat☆361Feb 17, 2026Updated 2 months ago
- The following repository contains code for all scRNAseq analysis and visualization performed in the paper: Single cell resolution analysi…☆18Oct 22, 2021Updated 4 years ago
- A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.☆94Jul 23, 2024Updated last year
- 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.
- Reference mapping for single-cell genomics☆404Mar 21, 2026Updated last month
- ENHANCE: Accurate denoising of single-cell RNA-Seq data (Python implementation)☆14Jun 5, 2019Updated 6 years ago
- Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)☆40Mar 31, 2026Updated last month
- identifying disease critical cell types and programs from single cell RNAseq☆58May 30, 2022Updated 3 years ago
- Bench-marking classification tools for scRNA-seq data☆196Jun 9, 2022Updated 3 years ago
- Single cell perturbation prediction☆342Dec 5, 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
- Python Implementation of MetaNeighbor scRNAseq Analysis Method☆10Nov 11, 2025Updated 5 months ago
- GREAT Analysis - Functional Enrichment on Genomic Regions☆98Jan 30, 2026Updated 3 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Python framework for single-cell RNA-seq clustering with special focus on transfer learning.☆18Aug 29, 2019Updated 6 years ago
- Code accompanying "The evolutionary history of 2,658 cancers", Nature 578, 122–128 (2020)☆17Jan 15, 2020Updated 6 years ago
- Reproduce analyses in Harmony Manuscript☆11Feb 21, 2020Updated 6 years ago
- Batch effect adjustment based on negative binomial regression for RNA sequencing count data☆205Sep 24, 2020Updated 5 years ago
- R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)☆36Dec 30, 2024Updated last year
- Comparison of single cell normalization strategies☆11Aug 13, 2021Updated 4 years ago
- scRNA-seq clustering, visualization, and differential expression pipeline from Sims Lab papers☆22Sep 28, 2021Updated 4 years ago