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

nextflow ATACseq pipeline for GG02

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

Scripts to index and align Bovine genome with HISAT2

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

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 workflow using FastQC, Bowtie2, SAMtools, featureCounts, R, and edgeR for differential gene expression analysis.

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 Nextflow DSL2 pipeline for reproducible RNA-seq analysis with automated reference retrieval and multi-aligner support.