🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.

Scripts to import your FeatureCounts output into DEXSeq

scripts for RNA-Seq analysis

RNA-seq Analysis Pipeline Testing and Optimization Resource - Intelligent pipeline selection and comprehensive benchmarking.

Quality Control, Mapping and Reads Count for RNA-Seq Analysis

This repository contatins a pipeline for RNA-Seq data processing using featurecounts for gene count generation

A tool for extraction of lexical features from text based on UIMA and MapReduce

This is a code tutorial for rna or dna sequence mapping by myself-RyanYip

Single-end RNA-seq pipeline: FastQC → Trimmomatic → HISAT2 → featureCounts. 93.98% alignment rate.

Scripts to index and align Bovine genome with HISAT2

nextflow ATACseq pipeline for GG02

This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.

RNA-seq expression and enrichment analysis of Pseudomonas aeruginosa (SigX mutant vs wild-type) using FastQC, fastp, STAR, featureCounts, DESeq2, and STRING to identify antibiotic stress-response pathways and key regulatory genes.

Minimal, production-ready Nextflow DSL2 RNA-seq pipeline for QC, alignment, gene counting, transcript quantification, coverage tracks, and matrix merging.

A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.

A pipeline to call intron and intergenic eRNAs from PRO-seq Data

Build Docker container for Subread package and (optionally) convert to Apptainer/Singularity.

This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.

Proof of concept of a RNA-Seq pipeline from reads to count matrix (including quality control) with Nextflow and additional example RNA-Seq analysis in R