An RNASeq snakemake workflow using the Tuxedo suite.
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Updated
Aug 19, 2019 - Python
An RNASeq snakemake workflow using the Tuxedo suite.
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
A basic pipeline for the analysis of RNASeq data. Entirely done in Bash and R script.
EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check http:https://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check http:https://research.libd.org/SPEAQeasy-example/.
Snakemake workflow for Salmon quantification and FastQC quality controls
RNA-Seq data analysis: whole transcriptome, stranded, dUTP method
An Automated RNASeq Analysis Pipeline (Differential expression to gene enrichment)
circs_snake : a snakemake-based circRNA detection workflow
miARma-seq: a comprehensive tool for miRNA, mRNA and circRNA analysis
A script to analyze with DESeq2 data from Kallisto. You maybe are interested only in DESeq2 part and its analisis and representation :)
Snakemake+singularity RNAseq processing pipeline
These snakefiles are prepared for the snakemake pipeline for the RNASeq analysis
Pipeline for calling and analyzing variants from RNA-Seq data
Docker Integrated Comparison of Alternative Splicing (AS) Tools. Benchmarking AS tools and genomic alignment tools.
Simple Snakemake RNA-Seq pipeline
Introduction to Bioinformatics workflows with Nextflow
In this repository : i have created RNAseq pipeline using snakemake rules
pilot pipeline that includes tool containerization
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