This RNAseq data analysis tutorial is created for educational purpose

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

A comprehensive pipeline for RNAseq data analysis

miARma-seq: a comprehensive tool for miRNA, mRNA and circRNA analysis

An Automated RNASeq Analysis Pipeline (Differential expression to gene enrichment)

Pipeline for generating RNAseq-based cancer patient reports

Docker Integrated Comparison of Alternative Splicing (AS) Tools. Benchmarking AS tools and genomic alignment tools.

lncRNA analysis pipeline

These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline

EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check http://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check http://research.libd.org/SPEAQeasy-example/.

iSofOrmS annoTAtoR pipeline

RNA-Seq data analysis: whole transcriptome, stranded, dUTP method

A python package for working with inputs to and outputs from the toil-rnaseq pipeline

circs_snake : a snakemake-based circRNA detection workflow

Snakemake workflow for Salmon quantification and FastQC quality controls

Pipeline for calling and analyzing variants from RNA-Seq data

These snakefiles are prepared for the snakemake pipeline for the RNASeq analysis

Snakemake+singularity RNAseq processing pipeline

pilot pipeline that includes tool containerization

RNA-seq replication analysis.