RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
☆1,229Mar 18, 2026Updated this week
Alternatives and similar repositories for rnaseq
Users that are interested in rnaseq 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…☆318Mar 17, 2026Updated last week
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆555Updated this week
- ATAC-seq peak-calling and QC analysis pipeline☆220Updated this week
- ChIP-seq peak-calling, QC and differential analysis pipeline.☆234Updated this week
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,430Mar 12, 2026Updated last week
- Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis inclu…☆1,419May 31, 2023Updated 2 years ago
- Nanopore demultiplexing, QC and alignment pipeline☆221Nov 20, 2025Updated 4 months ago
- A curated list of nextflow based pipelines☆622Jun 23, 2025Updated 9 months ago
- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair☆188Updated this week
- Pipeline to fetch metadata and raw FastQ files from public databases☆189Feb 8, 2026Updated last month
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,308Updated this week
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆91Updated this week
- A small-RNA sequencing analysis pipeline☆98Jan 7, 2026Updated 2 months ago
- RNAseq analysis notes from Ming Tang☆1,072Nov 15, 2021Updated 4 years ago
- A DSL for data-driven computational pipelines☆3,331Updated this week
- RNA-seq analysis pipeline for detection of gene-fusions☆172Updated this week
- Python package with helper tools for the nf-core community.☆295Mar 17, 2026Updated last week
- Repository to host tool-specific module files for the Nextflow DSL2 community!☆404Updated this week
- RNA-seq aligner☆2,162Mar 18, 2025Updated last year
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆870Mar 11, 2026Updated last week
- A repository for setting up a RNAseq workflow☆455Apr 10, 2017Updated 8 years ago
- Differential gene expression analysis and pathway analysis of RNAseq data☆32Jul 3, 2025Updated 8 months ago
- Customizable workflows based on snakemake and python for the analysis of NGS data☆400Mar 9, 2026Updated 2 weeks ago
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆567Jan 13, 2026Updated 2 months ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆831Feb 10, 2026Updated last month
- Config files used to define parameters specific to compute environments at different Institutions☆108Updated this week
- A curated collection of Nextflow implementation patterns☆369Nov 21, 2023Updated 2 years ago
- rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis☆63Jun 3, 2025Updated 9 months ago
- Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream …☆109Mar 16, 2026Updated last week
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,678Mar 9, 2026Updated 2 weeks ago
- RNA-seq workflow using STAR and DESeq2☆352Dec 18, 2025Updated 3 months ago
- Analysis of Chromosome Conformation Capture data (Hi-C)☆110Mar 6, 2026Updated 2 weeks ago
- FlowCraft: a component-based pipeline composer for omics analysis using Nextflow.☆248Aug 10, 2025Updated 7 months ago
- R toolkit for single cell genomics☆2,689Updated this week
- Test data to be used for automated testing with the nf-core pipelines☆154Updated this week
- Toolkit for processing sequences in FASTA/Q formats☆1,531Jun 1, 2025Updated 9 months ago
- Documentation and description of AWS iGenomes S3 resource.☆121Dec 8, 2024Updated last year
- Nextflow training material☆231Mar 17, 2026Updated last week
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆268Mar 15, 2026Updated last week