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