Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.
☆56Jun 1, 2025Updated 9 months ago
Alternatives and similar repositories for cna
Users that are interested in cna are comparing it to the libraries listed below
Sorting:
- R implementation of the Reshef and Rumker CNA method (https://github.com/immunogenomics/cna)☆15Aug 24, 2023Updated 2 years ago
- Pairwise Hierarchical Model☆20Mar 11, 2022Updated 3 years ago
- Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples withi…☆41Feb 8, 2023Updated 3 years ago
- Efficiently compute robust markers across single-cell datasets☆12Apr 21, 2021Updated 4 years ago
- Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).☆13Jan 12, 2024Updated 2 years ago
- ☆11May 30, 2023Updated 2 years ago
- A guide to using the Python scRNA-seq analysis package Scanpy from R☆15Apr 27, 2020Updated 5 years ago
- Reference mapping for single-cell genomics☆399Dec 2, 2025Updated 3 months ago
- Convert your single-cell/spatial analyses to parallel HPC/cloud workflows just using pipes in R☆17Dec 18, 2024Updated last year
- Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).☆88Dec 4, 2025Updated 2 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆378Jul 30, 2025Updated 7 months ago
- A Bayesian model for compositional single-cell data analysis☆188Jan 13, 2026Updated last month
- GESTALT processing pipeline for barcodes captured with single-cell RNA sequencing☆13Jan 26, 2020Updated 6 years ago
- ☆42Sep 14, 2022Updated 3 years ago
- AUCell: score single cells with gene regulatory networks☆185Mar 9, 2024Updated last year
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated 7 months ago
- Automated cell type classification☆116Jan 3, 2025Updated last year
- Port of symphony algorithm of single-cell reference atlas mapping to Python☆34Dec 11, 2025Updated 2 months ago
- A package to help convert different single-cell data formats to each other☆458Feb 20, 2026Updated last week
- R package implementation of Milo for testing for differential abundance in KNN graphs☆420Sep 4, 2025Updated 5 months ago
- ☆49Nov 28, 2025Updated 3 months ago
- R package to visualize gene expression data based on weighted kernel density estimation☆112Feb 6, 2026Updated 3 weeks ago
- cell type deconvolution for multi-condition bulk RNA-seq data☆31Feb 28, 2022Updated 4 years ago
- Methods for detecting doublets in single-cell sequencing data☆231Feb 12, 2026Updated 2 weeks ago
- Quantifying experimental perturbations at single cell resolution☆113Sep 27, 2024Updated last year
- ☆12Apr 26, 2021Updated 4 years ago
- Cell type prioritization in single-cell data☆138Oct 23, 2024Updated last year
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆219Feb 26, 2024Updated 2 years ago
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 4 months ago
- ☆35Dec 19, 2023Updated 2 years ago
- R package for pathway analysis in scRNA-seq data☆77Aug 17, 2024Updated last year
- Benchmarking analysis of data integration tools☆407Sep 17, 2025Updated 5 months ago
- Probabilistic single-cell pseudotime with Edward+Tensorflow☆12Oct 5, 2017Updated 8 years ago
- Multi-resolution Variational Inference☆22Updated this week
- BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/pa…☆87Sep 17, 2025Updated 5 months ago
- Querying cellular states and programs by learning representations of gene sets☆16Nov 2, 2025Updated 3 months ago
- Differential Correlation across Ranked Samples☆12May 31, 2023Updated 2 years ago
- ☆145Apr 19, 2025Updated 10 months ago
- A tool for unsupervised projection of single cell RNA-seq data☆97Nov 24, 2020Updated 5 years ago