A single cell transcriptomics pipeline for QC, integration and making the data presentable
☆85Feb 15, 2026Updated 2 weeks ago
Alternatives and similar repositories for scdownstream
Users that are interested in scdownstream are comparing it to the libraries listed below
Sorting:
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆89Updated this week
- Please consider using/contributing to https://github.com/nf-core/scdownstream☆26Jun 13, 2024Updated last year
- Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-dropl…☆313Updated this week
- A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq☆21Nov 20, 2025Updated 3 months ago
- Cookiecutter profile for making a NextFlow-based bioinformatics tool☆17Jul 8, 2024Updated last year
- Comprehensive pipeline for donor demultiplexing in single cell☆25Updated this week
- Customer workshop materials☆19May 11, 2023Updated 2 years ago
- gatk4 RNA variant calling pipeline☆59Feb 10, 2026Updated 3 weeks ago
- rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis☆63Jun 3, 2025Updated 9 months ago
- nf-core/references is a bioinformatics pipeline that build references, for multiple use cases☆19Jan 15, 2026Updated last month
- Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads☆32Nov 20, 2025Updated 3 months ago
- A collection of Groovy classes that provide utility services to nextflow pipelines.☆13Oct 25, 2022Updated 3 years ago
- Compare the quality of multiple genomes, along with their annotations.☆20Jan 15, 2026Updated last month
- Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and …☆20Feb 18, 2026Updated last week
- An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.☆31Updated this week
- A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted nex…☆56Feb 13, 2026Updated 2 weeks ago
- Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscript…☆18Feb 4, 2026Updated 3 weeks ago
- A bioinformatics best-practice analysis pipeline for epitope prediction and annotation☆51Updated this week
- A tutorial on how to create bioinformatics pipelines as bash scripts, Makefiles and using tools like Nextflow.☆16Nov 14, 2022Updated 3 years ago
- ☆27Jan 27, 2026Updated last month
- VCF Observer is a VCF file analysis, comparison, and visualization tool.☆18Jan 3, 2025Updated last year
- Params validation plugin for Nextflow pipelines☆48Aug 7, 2024Updated last year
- A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.☆40Nov 20, 2025Updated 3 months ago
- Simple bacterial assembly and annotation pipeline☆85Feb 23, 2026Updated last week
- Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research☆40Updated this week
- A docker image for single-cell analysis☆105Oct 24, 2025Updated 4 months ago
- ☆12Nov 7, 2025Updated 3 months ago
- Genomic Features in Python from BioConductor's AnnotationHub☆22Feb 23, 2026Updated last week
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆550Feb 24, 2026Updated last week
- RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.☆1,212Updated this week
- Network construction Algorithm☆22Sep 5, 2024Updated last year
- Data Science Operations (dso) command line tool☆46Sep 8, 2025Updated 5 months ago
- [Archived] SnakeMake pipeline to run BlobTools on public assemblies☆11Jul 3, 2023Updated 2 years ago
- Variational Auto Encoders for learning binding signatures of transcription factors☆14Mar 14, 2024Updated last year
- Nextflow Tower CLI tool☆52Updated this week
- Gene Ontology subgraph visualizations☆20Jan 6, 2026Updated last month
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…☆24Nov 20, 2025Updated 3 months ago
- A Nextflow workflow to generate lift over files for any pair of genomes☆69Nov 19, 2025Updated 3 months ago
- Repository to host tool-specific module files for the Nextflow DSL2 community!☆402Updated this week