There are 5 repositories under rna-seq-pipeline topic.
Analyze your RNA sequencing data without writing a single line of code
Single cell Nanopore sequencing data for Genotype and Phenotype
All-in-one analysis pipeline
Automatic Packaging and Distribution of Bioinformatics Pipelines
Automatic RNA-Seq Pipelines with Interactive Report
:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data
A quick recap of widely used differential analyses methods in R for RNA-seq experiments
A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)
Clair3-RNA - a long-read small variant caller for RNA sequencing data
A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments
Quality Control, Mapping and Reads Count for RNA-Seq Analysis
Materials for "Teaching Bioinformatics and R for dataviz course" June-August 2019 in Majorbio
Standard analysis routine for samples that were generated with Lexogen's QuantSeq pool library preparation kit.
A slurm based pipeline for RNA-seq analysis to execute on linux clusters. Feel free to connect to visualize your RNA-seq data on the clouds
Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository.
Viper is a Snakemake workflow, aimed at performing the RNA-seq workflow of the paper 'Causes and consequences of a glutamine induced normoxic HIF1 activity for the tumor metabolism', Kappler et al. (2019) in a reproducible and automated manner
Roddy RNA-seq Workflow Plugin
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.
De nove assembly and annotation of Fragilaria radians transcriptome
miRPipe: Open source RNA-Seq bioinformatics analysis docker for identification of miRNAs and piRNAs
Snakemake workflow for transposable element RNA-Seq using TEtranscripts
LSTrAP-denovo is an easy-to-use pipeline to assemble and annotate transcripts for species without genome / genomic annotations using publicly available RNA-seq data.
The power of the R's differential gene expression analysis packages, with no programming required.
DEWE (Differential Expression Workflow Executor) is an open source application for easily executing Differential Expression analyses in RNA-Seq data.