Standard analysis routine for samples that were generated with Lexogen's QuantSeq pool library preparation kit.

Automated RNA-seq pipeline for lncRNA indentification

Tool to identify chimeric events from RNA-Seq data

SmedAnno is a robust RNA-Seq annotation pipeline designed to streamline analysis from raw reads to a comprehensive, functionally annotated gene set. It handles short reads, long reads, or a combination of both, and provides extensive quality control metrics to help identify potentially fragmented or chimeric gene models.

Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.

In development scripts for EvolOMICs group's NGS Data Analysis Pipeline

This repository contains an automated shell script (run_pipeline.sh) for processing paired-end Bulk RNA-Seq data. The pipeline takes raw FASTQ files for a specified sample, performs quality control, trims poor-quality bases, aligns the reads to a reference genome, and quantifies gene expression.

An analysis script routine to assess if samples that were prepared with Lexogen's barcoded targeted QuantSeq Flex library preparation contain copies of the SARS-CoV-2 virus.

In this repository, I try to replicate the results of Rodriguez2017

This project uses an workflow pipeline to generate map and assemble RNAseq reads to a reference genome. Furthermore, we generate counts data and identify differentially expressed genes from 2 conditions.

It is a RNA-seq pipeline made as a mini project.

This repository contains all the scripts necessary to perform RNA-Seq analysis on HTC CRC Pitt.

Pipeline for processing bulk RNA-seq data from raw .fastq files to read counts.

End-to-end pipeline from raw FASTQ files to differentially expressed genes, built entirely from command-line tools on Linux. ~98% mapping rate across all samples and 1,192 significantly differentially express