Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
☆90Dec 4, 2025Updated 6 months ago
Alternatives and similar repositories for singleCellHaystack
Users that are interested in singleCellHaystack are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Comparison of dimensionality reduction methods☆30Mar 24, 2020Updated 6 years ago
- Collection of analysis methods for small count data generated by rafalab members (the methods, not the data).☆24Jul 10, 2024Updated last year
- Signature Analysis and Visualization for Single-Cell RNA-seq☆181Jun 10, 2024Updated 2 years ago
- Interpretation of cell states using reference single-cell maps☆323Dec 19, 2025Updated 6 months ago
- Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).☆13Jan 12, 2024Updated 2 years ago
- 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.
- COMET Single-Cell Marker Detection tool☆34Jun 21, 2022Updated 4 years ago
- post-clustering differential expression test☆37May 28, 2019Updated 7 years ago
- R API and htmlwidget for Vitessce☆45Aug 13, 2025Updated 10 months ago
- Introduction to single cell RNAseq data analysis and interpretation course work provided by Harvard Informatics Team.☆17Nov 20, 2018Updated 7 years ago
- Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)☆17Jun 28, 2025Updated last year
- Multi-sample multi-group scRNA-seq analysis tools☆235Jun 4, 2026Updated 3 weeks ago
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆228Jun 16, 2026Updated last week
- Spatial omics analysis toolbox☆377Jun 2, 2026Updated 3 weeks ago
- Cluster Identity Predictor (R package implementation)☆22Mar 8, 2022Updated 4 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Reproducibility for the "Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models" paper☆13Jul 15, 2022Updated 3 years ago
- R package for benchmarking single cell analysis methods☆33Oct 4, 2023Updated 2 years ago
- Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and…☆41Aug 23, 2023Updated 2 years ago
- Table of software for the analysis of single-cell RNA-seq data.☆339Updated this week
- Efficient and precise single-cell reference atlas mapping with Symphony☆123May 24, 2026Updated last month
- ☆31Apr 12, 2023Updated 3 years ago
- Batch balanced KNN☆178Oct 11, 2023Updated 2 years ago
- Demultiplexing pooled scRNA-seq data with or without genotype reference☆104Apr 11, 2025Updated last year
- R package of techniques for comparing clusterings of single-cell sequencing data☆41Apr 13, 2026Updated 2 months ago
- 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.
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated 11 months ago
- Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…☆57Jun 2, 2026Updated 3 weeks ago
- Detect doublets in single-cell RNA-seq data☆86Jul 3, 2019Updated 6 years ago
- An R package for multi-dimensional pathway enrichment analysis☆18Jan 8, 2026Updated 5 months ago
- Analysis of cell-cell communication at single-cell resolution☆107Sep 10, 2024Updated last year
- Identify genes with spatial expression trends in single-cell gene expression data☆51Mar 20, 2018Updated 8 years ago
- Multi-sample Unified Discriminant ANalysis☆75Apr 11, 2023Updated 3 years ago
- Build predicted cell-cell interaction networks from single-cell data.☆10Jan 31, 2023Updated 3 years ago
- Seurat meets tidyverse. The best of both worlds.☆166Mar 3, 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.
- Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.☆15Jul 16, 2023Updated 2 years ago
- Scalable, downsampling-free automated cell-population discovery, feature engineering, classification and visualization of single-cell (mo…☆12Aug 30, 2021Updated 4 years ago
- A method for calculating single cell entropy and reconstructing cell differentiation lineage using single-cell RNA-seq data☆10May 26, 2023Updated 3 years ago
- Convert your single-cell/spatial analyses to parallel HPC/cloud workflows just using pipes in R☆18May 19, 2026Updated last month
- Single-Cell Clustering Assessment Framework☆110Oct 27, 2023Updated 2 years ago
- ☆12Aug 23, 2018Updated 7 years ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆661Jun 5, 2026Updated 3 weeks ago