Please consider using/contributing to https://github.com/nf-core/scdownstream
☆26Jun 13, 2024Updated 2 years ago
Alternatives and similar repositories for scflow
Users that are interested in scflow are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-dropl…☆350Aug 5, 2026Updated 3 weeks ago
- Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.☆25Jul 28, 2026Updated last month
- A single cell transcriptomics pipeline for QC, integration and making the data presentable☆113Updated this week
- Examples showing how to configure Nextflow to run with Wave containers provisioning service☆21Aug 10, 2026Updated 3 weeks ago
- ☆10Nov 4, 2021Updated 4 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- A pipeline for droplet-based single-cell RNA-seq and spot-based spatial transcriptomics data secondary analysis implemented in the drake …☆17Aug 27, 2025Updated last year
- A repository of pipelines for single-cell data in Nextflow DSL2☆81Apr 19, 2023Updated 3 years ago
- Code for the paper on t-SNE with variable degree of freedom☆11Jun 27, 2019Updated 7 years ago
- Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines☆47Mar 13, 2025Updated last year
- The NanoPipe pipeline analyzes reads generated by the Oxford Nanopore sequencing devices. As a result, it provides alignments to any targ…☆18Dec 21, 2018Updated 7 years ago
- Estimate the cis-regulatory activity of transposable element (TEs) subfamilies☆12Dec 15, 2023Updated 2 years ago
- Northern Arizona SNP Pipeline☆20Oct 29, 2024Updated last year
- Easy single cell analysis platform for enrichment☆231Aug 9, 2026Updated 3 weeks ago
- ☆39Apr 21, 2026Updated 4 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Statistics: Data analysis and modelling☆17Sep 22, 2025Updated 11 months ago
- Analysis of Single Cell Expression, Normalization and Differential expression☆14Feb 29, 2020Updated 6 years ago
- Python implementation and field-tool for automated pipeline launching through Tower CLI (beta)☆36Aug 10, 2026Updated 3 weeks ago
- Feature selection for preserving biological trajectories in single-cell data☆21Jun 24, 2026Updated 2 months ago
- Code used to carry out parameter estimation, correlation estimation, type 1 error analysis, and power analysis for our "Pseudoreplication…☆21Sep 9, 2020Updated 5 years ago
- https://molecular-neurogenetics.github.io/truster/☆12Jul 14, 2025Updated last year
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆71Apr 24, 2026Updated 4 months ago
- A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.☆69Aug 17, 2026Updated 2 weeks ago
- A web tool to do automatic spots detections and positional adjustments for Spatial Transcriptomics Datasets.☆26Nov 17, 2022Updated 3 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A Grammar of Data Manipulation for Omics Data☆21Aug 31, 2020Updated 6 years ago
- Using Bulk Gene Expression to Estimate Cell-Type-Specific Gene Expression via Deconvolution☆47May 3, 2023Updated 3 years ago
- Learning cell communication from spatial graphs of cells☆121Jan 15, 2024Updated 2 years ago
- Detection, colocalization, and quantification of spots / puncta☆17Mar 22, 2023Updated 3 years ago
- Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline☆48Jun 12, 2023Updated 3 years ago
- Visualisation and prioritisation of genomic variants from human exome sequencing projects☆13Apr 23, 2019Updated 7 years ago
- ☆13Mar 29, 2024Updated 2 years ago
- Hierarchical graph clustering☆38Jun 22, 2018Updated 8 years ago
- GenUI frontend application. It provides a GUI to the GenUI REST API web services.☆23Sep 4, 2023Updated 2 years ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Cookiecutter profile for making a NextFlow-based bioinformatics tool☆17Jul 8, 2024Updated 2 years ago
- Visualise interstrain recombination from environmental samples.☆28Apr 18, 2019Updated 7 years ago
- Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products☆37Aug 18, 2026Updated 2 weeks ago
- Collection of Sphinx extensions similar to (but more flexible than) numpydoc☆12Aug 25, 2026Updated last week
- Python package with helper tools for the nf-core community.☆319Aug 25, 2026Updated last week
- R package for single cell and other data analysis using diffusion maps☆109Jul 22, 2026Updated last month
- ☆12Aug 23, 2018Updated 8 years ago