kharchenkolab / pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
☆223Updated last year
Alternatives and similar repositories for pagoda2:
Users that are interested in pagoda2 are comparing it to the libraries listed below
- LIANA: a LIgand-receptor ANalysis frAmework☆196Updated 7 months ago
- An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.☆161Updated last year
- Methods for detecting doublets in single-cell sequencing data☆184Updated this week
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆266Updated 2 years ago
- Interactively analyze single cell genomic data☆182Updated last month
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆226Updated last year
- Tools and methods for analysis of single cell assay data in R☆232Updated last year
- Generate high quality, publication ready visualizations for single cell transcriptomics data.☆178Updated last month
- Multi-sample multi-group scRNA-seq analysis tools☆182Updated last month
- Conversion between scRNA-seq objects☆164Updated this week
- SingleCellNet: classify single cells across species and platforms☆136Updated last year
- Gene set variation analysis☆213Updated this week
- Clone of the Bioconductor repository for the SingleR package.☆185Updated last month
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆140Updated 2 months ago
- Signature Analysis and Visualization for Single-Cell RNA-seq☆165Updated 9 months ago
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆286Updated 11 months ago
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆205Updated last year
- Interpretation of cell states using reference single-cell maps☆269Updated 3 weeks ago
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆221Updated 3 months ago
- A toolkit for single-cell immune profiling☆328Updated this week
- ☆162Updated 6 months ago
- A guide to using a Seurat object in conjunction with RNA Velocity☆137Updated 3 years ago
- Multiome GRN inference.☆119Updated 11 months ago
- This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data☆121Updated 2 years ago
- R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆247Updated this week
- Multi-subject Single Cell Deconvolution☆249Updated last year
- Fast Wilcoxon and auROC☆176Updated 4 months ago
- Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods☆91Updated 2 years ago
- A Bayesian model for compositional single-cell data analysis☆158Updated last year
- Significance analysis for clustering single-cell RNA-sequencing data☆113Updated 6 months ago