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

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.

Pipeline for generating RNAseq-based cancer patient reports

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

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).

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

lncRNA analysis pipeline

RNAseq analysis workflow

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.

An easy pipeline to analyze data with Salmon.

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

Snakemake+singularity RNAseq processing pipeline

pilot pipeline that includes tool containerization

RNA-seq benchmarking toolkit including UTR annotation, quantification (STAR+Salmon, Salmon, Kallisto), multimapping evaluation, and optional simulation scripts.

HULK is a fully automated, containerized pipeline for processing bulk RNA-seq data directly from SRA accessions

Endometriosis is a severely understudied gynecological disorder affecting approximately 5%-10% of women. This project showcases the need for more research regarding women’s health, with a particular emphasis on endometriosis.

Snakemake workflow for Salmon quantification and FastQC quality controls

RNA-seq for rare diseases pipeline using nextflow

Pipeline for calling and analyzing variants from RNA-Seq data

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

circs_snake : a snakemake-based circRNA detection workflow

🧬Custom Bulk RNA-seq workflow for QC, DESeq2 differential expression, and visualization in R 🧬 (RNA-seq, bioinformatics, bulk-rnaseq, visualization, DESeq2, edgeR)

A comprehensive Nextflow pipeline for RNA-seq data analysis, encompassing quality control, read alignment, quantification, and differential expression analysis.

A book that discusses topics and contains tutorials relevant to population genomics