A pipeline for droplet-based single-cell RNA-seq and spot-based spatial transcriptomics data secondary analysis implemented in the drake Make-like pipeline toolkit for the R language.
☆17Aug 27, 2025Updated last year
Alternatives and similar repositories for scdrake
Users that are interested in scdrake are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆84Jan 23, 2025Updated last year
- Code for a multimodal atlas of healthy and injured cell states and niches in the human kidney☆27Mar 7, 2024Updated 2 years ago
- Scripts to help get fastqs☆19May 13, 2026Updated 4 months ago
- Please consider using/contributing to https://github.com/nf-core/scdownstream☆26Jun 13, 2024Updated 2 years ago
- Development repository for R package 'PLSDAbatch ' hosted on Bioconductor.☆16Jun 26, 2026Updated 3 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Building on material from Introduction to Single Cell RNA-Seq, this workshop aims to cover advanced topics, including TCR and trajectory …☆15Apr 12, 2023Updated 3 years ago
- A single-cell RNA-seq pipeline☆28Apr 12, 2023Updated 3 years ago
- ☆11May 14, 2025Updated last year
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆95Sep 8, 2026Updated 2 weeks ago
- Multi-modal single cell analysis pipelines☆63Dec 11, 2025Updated 9 months ago
- collections of tools for cytometry data analysis☆14Jul 9, 2020Updated 6 years ago
- The Singularity Community Catalog of Singularity* recipe files.☆11Oct 27, 2025Updated 11 months ago
- Spatial Tumor Microenvironment (SpatialTME) database is a comprehensive database designed for characterize tumor spatial microenvironment…☆13Dec 4, 2023Updated 2 years ago
- Analaysis for the batch correction paper☆12Apr 26, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Fast, modular and reproducible generation of publication quality scientific figures and movies with only a few lines of code.☆17Apr 9, 2025Updated last year
- CUDA implementation of RTXX algorithm for multiplication of matrix and its transpose X^T X☆19Jun 9, 2025Updated last year
- Image converter from multiple formats to PDF - useful script for scientific writing e.g. in LaTeX☆10Oct 15, 2017Updated 8 years ago
- Cross-modal Identification of Tertiary Lymphoid Structures☆30Jun 19, 2024Updated 2 years ago
- Single-cell analytic toolbox that offers modular workflows for multi-level cellular annotation and user-friendly analysis reports☆11Mar 31, 2026Updated 5 months ago
- ☆12Sep 7, 2023Updated 3 years ago
- ☆14Feb 17, 2022Updated 4 years ago
- A repository for benchmarking spatial deconvolution and mapping tools☆37May 13, 2025Updated last year
- Significance analysis for clustering single-cell RNA-sequencing data☆128Sep 7, 2024Updated 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.
- ☆12Mar 22, 2024Updated 2 years ago
- NGS perl modules☆10Updated this week
- A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)☆14Sep 1, 2026Updated 3 weeks ago
- Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data☆11Sep 3, 2025Updated last year
- Semestral project for the subject Methods of computational inteligence @ fit.cvut.cz☆22Jan 31, 2017Updated 9 years ago
- ☆11Mar 2, 2021Updated 5 years ago
- aCcelerated Alignment-FrEe sequence analysis☆12May 8, 2018Updated 8 years ago
- ☆10Feb 5, 2026Updated 7 months ago
- an empirical Bayesian framework for mutation detection from cancer genome sequencing data☆31Apr 5, 2016Updated 10 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Visualizing Somatic Alterations of 10X Spatial Transcriptomics Data☆16Nov 7, 2024Updated last year
- Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Iso…☆41May 6, 2024Updated 2 years ago
- R package implementing a simple method for CD8 T cell epitope prediction by MHC class I binding for HLA and other MHC-I molecules.☆15Sep 21, 2020Updated 6 years ago
- A manually curated lists of software, publications and other resources related to the analysis of HDX-MS data.☆13Dec 15, 2025Updated 9 months ago
- Free, open source crypto trading bot☆23Dec 7, 2024Updated last year
- ☆14Mar 18, 2022Updated 4 years ago
- A pipeline for scRNA analysis under HPC☆11Jul 15, 2024Updated 2 years ago