🔬 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

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

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

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

Scripts to index and align Bovine genome with HISAT2

nextflow ATACseq pipeline for GG02

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

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

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