featurecounts

🔬 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.

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

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

A complete bioinformatics pipeline (FastQC, fastp, HISAT2, featureCounts, DESeq2) for RNA-Seq DGE analysis of Klebsiella pneumoniae (WT vs. ΔcpxR).

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

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.

Rust-based exon counting optimized for RNA-seq

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

End-to-end bulk RNA-seq analysis pipeline for HPC clusters (Nextflow + Snakemake) | QC → Trimming → Mapping → Quantification

Containerized Snakemake workflow for RNA-seq: HISAT2 + featureCounts gene counts, Salmon transcript quantification, and comprehensive QC (FastQC, fastp, Picard, Qualimap, RSeQC, MultiQC). On-demand index building; Docker & Apptainer ready.

Modular Bash pipeline from an SRA accession to a gene-level count matrix: fastp trimming, HISAT2 alignment, featureCounts quantification, with per-stage QC.

An automated, end-to-end RNA-Seq preprocessing and quantification pipeline utilizing HISAT2 for genomic alignment and featureCounts for gene expression matrix generation. It is optimized for VMware.

RNA seq analysis on P. Aeruginosa PAO1 Control vs Heat Shock Treatment