RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

A single-cell RNAseq pipeline for 10X genomics data

RNA-seq analysis pipeline for detection of gene-fusions

GATK RNA-Seq Variant Calling in Nextflow

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

See the main fork of this repository here >>>

An automated RNA-seq pipeline using Nextflow

A proof of concept RNA-Seq pipeline with Nextflow

A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

Master of Pores 2

Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

Nextflow pipeline for BWA, BWA2 and STAR alignments

A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq

Nextflow pipeline dedicated to RiboMethSeq data processing

RNA-Seq pipeline