A repository of pipelines for single-cell data in Nextflow DSL2
☆81Apr 19, 2023Updated 2 years ago
Alternatives and similar repositories for vsn-pipelines
Users that are interested in vsn-pipelines are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Fast visualization tool for large-scale and high dimensional single-cell data☆78Dec 16, 2025Updated 3 months ago
- An R package designed to demultiplex cell hashing data☆31Feb 10, 2026Updated last month
- ☆22May 6, 2022Updated 3 years ago
- R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters an…☆48Apr 8, 2022Updated 4 years ago
- Luslab nextflow modules☆14Apr 30, 2021Updated 4 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.
- Please consider using/contributing to https://github.com/nf-core/scdownstream☆26Jun 13, 2024Updated last year
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆319Nov 1, 2022Updated 3 years ago
- cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data☆145Apr 5, 2024Updated 2 years ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆184Mar 27, 2025Updated last year
- Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments☆10Mar 13, 2021Updated 5 years ago
- A collection of project templates and useful functions for single-cell data analysis with Scanpy.☆21Jun 12, 2023Updated 2 years ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆594Jun 26, 2025Updated 9 months ago
- Detecting Aberrant Splicing Events from RNA-sequencing data☆16Dec 10, 2024Updated last year
- A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…☆58May 5, 2021Updated 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 and start building anything your business needs.
- ☆11Sep 7, 2023Updated 2 years ago
- ☆18Oct 22, 2024Updated last year
- ☆19Dec 15, 2023Updated 2 years ago
- Quantifying experimental perturbations at single cell resolution☆114Sep 27, 2024Updated last year
- ScoMAP is an R package to spatially integrate single-cell omics data into virtual cells and infer enhancer-to-gene relationships.☆29Oct 4, 2021Updated 4 years ago
- A tool for semi-automatic cell type classification☆464Mar 21, 2026Updated 2 weeks ago
- RNA Velocity generalized through dynamical modeling☆495Feb 25, 2026Updated last month
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆67Mar 31, 2026Updated last week
- "The who the what the huh?" is our pipeline for converting bcl files to fastq and performing QC.☆11Sep 19, 2022Updated 3 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- data and model repository for single-cell data☆136Dec 21, 2023Updated 2 years ago
- Code to reproduce analyses and figures for Kamath et al., 2022☆12May 5, 2022Updated 3 years ago
- BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis☆50Mar 26, 2026Updated 2 weeks ago
- Nextflow workflow for automatic repeat detection, classification and masking☆13Feb 19, 2018Updated 8 years ago
- ☆15Jun 3, 2019Updated 6 years ago
- Work with trained factor models in Python☆39Oct 22, 2024Updated last year
- Scripts and notebooks to reproduce all analysis from Massoni-Badosa et al. (2022)☆36Jan 8, 2025Updated last year
- Scripts associated with the 2023 Open Problems competition☆11Nov 23, 2023Updated 2 years ago
- Demultiplexing pooled scRNA-seq data with or without genotype reference☆98Apr 11, 2025Updated 11 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- iCellR is an interactive R package designed to facilitate the analysis and visualization of high-throughput single-cell sequencing data. …☆128Nov 10, 2025Updated 4 months ago
- Multi-sample multi-group scRNA-seq analysis tools☆222Mar 25, 2026Updated 2 weeks ago
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆250Jan 16, 2026Updated 2 months ago
- Port of symphony algorithm of single-cell reference atlas mapping to Python☆33Mar 16, 2026Updated 3 weeks ago
- A set of files to do genomics analysis on python☆18Jun 5, 2025Updated 10 months ago
- A python implementation of scran computeSumFactors: normalization by deconvolution for single-cell RNA-sequencing☆33Nov 4, 2023Updated 2 years ago
- A scalable SCENIC workflow for single-cell gene regulatory network analysis☆174Dec 8, 2022Updated 3 years ago