R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
☆259Jun 28, 2026Updated 2 months ago
Alternatives and similar repositories for pagoda2
Users that are interested in pagoda2 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 the joint analysis of multiple single-cell RNA-seq datasets☆231Jul 2, 2026Updated 2 months ago
- AUCell: score single cells with gene regulatory networks☆205Mar 9, 2024Updated 2 years ago
- R package for analyzing single-cell RNA-seq data☆180Feb 29, 2024Updated 2 years ago
- scPred package for cell type prediction from scRNA-seq data☆107Jan 18, 2024Updated 2 years ago
- Easy single cell analysis platform for enrichment☆234Aug 9, 2026Updated last month
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- ☆315Nov 10, 2024Updated last year
- Interactively analyze single cell genomic data☆189Updated this week
- NicheNet: predict active ligand-target links between interacting cells☆680Updated this week
- LIANA: a LIgand-receptor ANalysis frAmework☆250Aug 7, 2024Updated 2 years ago
- Methods for detecting doublets in single-cell sequencing data☆270Aug 31, 2026Updated 3 weeks ago
- R package for integrating and analyzing multiple single-cell datasets☆433Aug 18, 2026Updated last month
- Interpretation of cell states using reference single-cell maps☆326Dec 19, 2025Updated 9 months ago
- Tools and methods for analysis of single cell assay data in R☆265Oct 17, 2025Updated 11 months ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆672Jun 5, 2026Updated 3 months ago
- 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.
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆343Nov 1, 2022Updated 3 years ago
- R package for detecting doublets in single-cell RNA sequencing data☆567Mar 21, 2025Updated last year
- R toolkit for the analysis of single-cell chromatin data☆428Sep 11, 2026Updated 2 weeks ago
- Inferring CNV from Single-Cell RNA-Seq☆684Nov 14, 2025Updated 10 months ago
- TRAjectory-based Differential Expression analysis for SEQuencing data☆314Jun 17, 2025Updated last year
- marker-based purification of cell types from single-cell RNA-seq datasets☆146Mar 13, 2026Updated 6 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆423Sep 12, 2026Updated 2 weeks ago
- RNA velocity estimation in R☆196Sep 14, 2023Updated 3 years ago
- A package to help convert different single-cell data formats to each other☆471Feb 20, 2026Updated 7 months ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Scissor package☆277May 10, 2024Updated 2 years ago
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆230Feb 4, 2026Updated 7 months ago
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆247May 8, 2023Updated 3 years ago
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆186Jun 24, 2021Updated 5 years ago
- Pipeline for initial analysis of droplet-based single-cell RNA-seq data☆94Jun 22, 2022Updated 4 years ago
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆271Jan 10, 2026Updated 8 months ago
- An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.☆179Jan 26, 2024Updated 2 years ago
- Automated cell type classification☆117Jan 3, 2025Updated last year
- ☆293Jul 15, 2022Updated 4 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Methods to discover gene programs on single-cell data☆211Sep 18, 2026Updated last week
- Gene set variation analysis☆249Updated this week
- iCellR is an interactive R package designed to facilitate the analysis and visualization of high-throughput single-cell sequencing data. …☆126Nov 10, 2025Updated 10 months ago
- R package to infer biological activities from omics data using a collection of methods.☆310Dec 16, 2025Updated 9 months ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆793Jan 6, 2024Updated 2 years ago
- ☆467Updated this week
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆348Apr 23, 2024Updated 2 years ago