Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
☆326May 15, 2026Updated last week
Alternatives and similar repositories for scrnaseq
Users that are interested in scrnaseq are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.☆1,291May 12, 2026Updated 2 weeks ago
- A single cell transcriptomics pipeline for QC, integration and making the data presentable☆102Updated this week
- ATAC-seq peak-calling and QC analysis pipeline☆224Updated this week
- Nascent Transcription Processing Pipeline☆22Apr 30, 2026Updated 3 weeks ago
- Please consider using/contributing to https://github.com/nf-core/scdownstream☆26Jun 13, 2024Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- ChIP-seq peak-calling, QC and differential analysis pipeline.☆240Updated this week
- RNA-seq analysis pipeline for detection of gene-fusions☆174Updated this week
- Pipeline to fetch metadata and raw FastQ files from public databases☆192Apr 30, 2026Updated 3 weeks ago
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆572Updated this week
- Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics☆54May 5, 2026Updated 3 weeks ago
- Demultiplexing pipeline for sequencing data☆54May 11, 2026Updated 2 weeks ago
- Nanopore demultiplexing, QC and alignment pipeline☆226Apr 30, 2026Updated 3 weeks ago
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆95Updated this week
- A small-RNA sequencing analysis pipeline☆99May 8, 2026Updated 2 weeks ago
- 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.
- Proteomics label-free quantification (LFQ) analysis pipeline☆37Jan 13, 2025Updated last year
- ScaleBio Single-cell RNA Nextflow Workflow☆40Jul 2, 2025Updated 10 months ago
- Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream …☆110May 14, 2026Updated last week
- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair☆192Apr 30, 2026Updated 3 weeks ago
- A docker image for single-cell analysis☆108Apr 18, 2026Updated last month
- Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)☆28Apr 30, 2026Updated 3 weeks ago
- gatk4 RNA variant calling pipeline☆60May 4, 2026Updated 3 weeks ago
- Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…☆75May 7, 2026Updated 2 weeks ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆472Jun 6, 2025Updated 11 months 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.
- Converts bam or cram files to fastq format and does quality control.☆31May 13, 2026Updated last week
- Python package with helper tools for the nf-core community.☆308May 19, 2026Updated last week
- Test data to be used for automated testing with the nf-core pipelines☆162Updated this week
- Call and score variants from WGS/WES of rare disease patients.☆117Updated this week
- Nextflow training material☆243May 16, 2026Updated last week
- An interactive explorer for single-cell transcriptomics data