A single cell transcriptomics pipeline for QC, integration and making the data presentable
☆93Apr 16, 2026Updated 2 weeks ago
Alternatives and similar repositories for scdownstream
Users that are interested in scdownstream are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Comprehensive pipeline for donor demultiplexing in single cell☆25Updated this week
- Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-dropl…☆323Mar 25, 2026Updated last month
- Please consider using/contributing to https://github.com/nf-core/scdownstream☆26Jun 13, 2024Updated last year
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆92Updated this week
- Cookiecutter profile for making a NextFlow-based bioinformatics tool☆17Jul 8, 2024Updated last year
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- nf-core/references is a bioinformatics pipeline that build references, for multiple use cases☆19Updated this week
- An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.☆31Feb 28, 2026Updated 2 months ago
- ☆31Updated this week
- A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq☆24Updated this week
- Customer workshop materials☆19Apr 16, 2026Updated 2 weeks ago
- rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis☆63Jun 3, 2025Updated 11 months ago
- Data Science Operations (dso) command line tool☆46Apr 13, 2026Updated 2 weeks ago
- A docker image for single-cell analysis☆107Apr 18, 2026Updated 2 weeks ago
- Network construction Algorithm☆22Sep 5, 2024Updated 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.
- gatk4 RNA variant calling pipeline☆60Apr 24, 2026Updated last week
- Params validation plugin for Nextflow pipelines☆48Aug 7, 2024Updated last year
- A bioinformatics best-practice analysis pipeline for epitope prediction and annotation☆51Apr 17, 2026Updated 2 weeks ago
- A nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis☆11May 9, 2024Updated last year
- A tutorial on how to create bioinformatics pipelines as bash scripts, Makefiles and using tools like Nextflow.☆16Nov 14, 2022Updated 3 years ago
- RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.☆1,271Updated this week
- ☆12Nov 7, 2025Updated 5 months ago
- A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)☆13Updated this week
- ☆27Jul 2, 2024Updated 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.
- Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data☆53Jan 12, 2024Updated 2 years ago
- Gene regulatory network containing signed transcription factor-target gene interactions☆106May 27, 2025Updated 11 months ago
- Bioinformatics pipeline to identify differentially active transcription factors between conditions using expression and epigenetic data☆14Mar 12, 2024Updated 2 years ago
- Container class to represent genomic locations and support genomic analysis☆27Updated this week
- A tool for semi-automatic cell type classification☆473Mar 21, 2026Updated last month
- A pipeline for droplet-based single-cell RNA-seq and spot-based spatial transcriptomics data secondary analysis implemented in the drake …☆16Aug 27, 2025Updated 8 months ago
- ☆12Jul 31, 2025Updated 9 months ago
- ☆11May 25, 2025Updated 11 months ago
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆563Apr 21, 2026Updated last week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research☆46Updated this week
- Test data to be used for automated testing with the nf-core pipelines☆160Updated this week
- Gene set scoring for single-cell data☆192Feb 11, 2026Updated 2 months ago
- A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted nex…☆57Mar 6, 2026Updated last month
- Visualizing Somatic Alterations of 10X Spatial Transcriptomics Data☆14Nov 7, 2024Updated last year
- VCF Observer is a VCF file analysis, comparison, and visualization tool.☆21Jan 3, 2025Updated last year
- Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…☆74Apr 17, 2026Updated 2 weeks ago