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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
A complete, reproducible bulk RNA-seq pipeline from raw FASTQ files to differential gene expression — built on a real published dataset, with every command tested and verified on macOS.
miARma-seq: a comprehensive tool for miRNA, mRNA and circRNA analysis
An Automated RNASeq Analysis Pipeline (Differential expression to gene enrichment)
Docker Integrated Comparison of Alternative Splicing (AS) Tools. Benchmarking AS tools and genomic alignment tools.
iSofOrmS annoTAtoR pipeline Aucouturier, C., Soirat, N., Castéra, L. et al. Fine mapping of RNA isoform diversity using an innovative targeted long-read RNA sequencing protocol with novel dedicated bioinformatics pipeline. BMC Genomics 25, 909 (2024).
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
Done as a summary of things that I learned in IBG summer internship. It contains a RNA-seq Nextflow pipeline for later data analysis and workflow management. It can go through quality control, trimming, indexing, alignment and statistical analysis.
A python package for working with inputs to and outputs from the toil-rnaseq pipeline
Snakemake+singularity RNAseq processing pipeline
RNA-seq benchmarking toolkit including UTR annotation, quantification (STAR+Salmon, Salmon, Kallisto), multimapping evaluation, and optional simulation scripts.
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