R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
☆246Aug 18, 2025Updated 6 months ago
Alternatives and similar repositories for pagoda2
Users that are interested in pagoda2 are comparing it to the libraries listed below
Sorting:
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆219Feb 26, 2024Updated 2 years ago
- AUCell: score single cells with gene regulatory networks☆185Mar 9, 2024Updated 2 years ago
- scPred package for cell type prediction from scRNA-seq data☆98Jan 18, 2024Updated 2 years ago
- R package for analyzing single-cell RNA-seq data☆179Feb 29, 2024Updated 2 years ago
- Interactively analyze single cell genomic data☆185Jan 14, 2026Updated last month
- Easy single cell analysis platform for enrichment☆216Jan 4, 2026Updated 2 months ago
- R package for integrating and analyzing multiple single-cell datasets☆424Feb 4, 2026Updated last month
- Tools and methods for analysis of single cell assay data in R☆261Oct 17, 2025Updated 4 months ago
- NicheNet: predict active ligand-target links between interacting cells☆620Nov 12, 2025Updated 3 months ago
- LIANA: a LIgand-receptor ANalysis frAmework☆233Aug 7, 2024Updated last year
- ☆285Nov 10, 2024Updated last year
- Fast, sensitive and accurate integration of single-cell data with Harmony☆622Oct 10, 2025Updated 4 months ago
- TRAjectory-based Differential Expression analysis for SEQuencing data☆290Jun 17, 2025Updated 8 months ago
- Interpretation of cell states using reference single-cell maps☆312Dec 19, 2025Updated 2 months ago
- Methods for detecting doublets in single-cell sequencing data☆231Feb 12, 2026Updated 3 weeks ago
- R toolkit for the analysis of single-cell chromatin data☆407Jan 20, 2026Updated last month
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆315Nov 1, 2022Updated 3 years ago
- Automated cell type classification☆116Jan 3, 2025Updated last year
- Scissor package☆253May 10, 2024Updated last year
- R package for detecting doublets in single-cell RNA sequencing data☆526Mar 21, 2025Updated 11 months ago
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆251Jan 10, 2026Updated last month
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆205Feb 4, 2026Updated last month
- A toolkit for single-cell immune profiling☆363Feb 28, 2026Updated last week
- RNA velocity estimation in R☆194Sep 14, 2023Updated 2 years ago
- A package to help convert different single-cell data formats to each other☆458Feb 20, 2026Updated 2 weeks ago
- Inferring CNV from Single-Cell RNA-Seq☆653Nov 14, 2025Updated 3 months ago
- ☆442Jan 8, 2026Updated 2 months ago
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆185Jun 24, 2021Updated 4 years ago
- Gene set variation analysis☆232Feb 25, 2026Updated last week
- An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.☆170Jan 26, 2024Updated 2 years ago
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆238May 8, 2023Updated 2 years ago
- marker-based purification of cell types from single-cell RNA-seq datasets☆141Jul 23, 2025Updated 7 months ago
- Multi-sample multi-group scRNA-seq analysis tools☆219Updated this week
- R package to infer biological activities from omics data using a collection of methods.☆286Dec 16, 2025Updated 2 months ago
- Pipeline for initial analysis of droplet-based single-cell RNA-seq data☆95Jun 22, 2022Updated 3 years ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆765Jan 6, 2024Updated 2 years ago
- Multi-subject Single Cell Deconvolution☆287Mar 4, 2024Updated 2 years ago
- iCellR is an interactive R package designed to facilitate the analysis and visualization of high-throughput single-cell sequencing data. …☆128Nov 10, 2025Updated 3 months ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆422Sep 4, 2025Updated 6 months ago