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.
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/.
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
These snakefiles are prepared for the snakemake pipeline for the RNASeq analysis
Snakemake+singularity RNAseq processing pipeline
pilot pipeline that includes tool containerization
Pipeline for calling and analyzing variants from RNA-Seq data
RNA-seq replication analysis.
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