Bioinformatics Tools and Blogs

Welcome to a Unified Portal for Omics Analysis

This portal provides a professionally curated suite of bioinformatics pipelines designed for scalable, reproducible, and modular analysis of high-throughput omics data. Developed and maintained with a focus on scientific transparency and code reusability, these pipelines are applicable across genomics, epigenomics, and transcriptomics studies.

All pipelines follow best practices and are version-controlled, with configuration files and usage instructions suitable for both core facilities and independent researchers. Below is an overview of the supported workflows:

• RNA-seq Pipeline: Supports alignment with STAR or quantification with Salmon, followed by count matrix generation, differential expression analysis using DESeq2, and pathway enrichment via GSEA or ORA. Quality control is performed using FastQC and MultiQC.
• DNA Methylation (EPIC Array) Pipeline: Provides preprocessing of IDATs, probe filtering, normalization (SWAN/BMIQ), and differential methylation analysis with limma. Downstream enrichment uses curated MSigDB gene sets.
• ATAC-seq Pipeline: Enables read alignment, peak calling with MACS2, transcription factor footprinting, and chromatin accessibility profiling. Designed for integration with RNA-seq and ChIP-seq data.
• ChIP-seq Pipeline: Processes transcription factor or histone modification data. Includes alignment, peak calling, motif enrichment, and browser-ready track generation for downstream interpretation.
• Cut&Tag Pipeline: Processes low-input chromatin data with Bowtie2 alignment and peak calling using SEACR or MACS2. Supports visualization and comparative analysis across conditions.
• Single-Cell Omics Pipeline: Integrates scRNA-seq, CITE-seq, and TCR/BCR-seq data. Includes preprocessing, ADT normalization, dimensionality reduction, clustering, and clonal expansion analysis using tools like Seurat and scRepertoire.
• WGBS Pipeline: Tailored for whole-genome bisulfite sequencing. Supports alignment with Bismark, methylation extraction, and downstream differential analysis using DSS or methylKit, with metaplot generation and tiling reports.
• WGS/WES Variant Calling Pipeline: Provides a complete workflow for both germline and somatic variant detection using BWA-MEM and GATK best practices. Includes recalibration, joint genotyping, filtration, and annotation using VEP or ANNOVAR.
• HiPlex Demultiplexer: Specialized for Cut&Tag libraries with multiplexed antibody and sample barcodes. Supports dual-layer demultiplexing (i7/i5 and 5′/3′ barcodes) and resolves homo- and hetero-combinations across FASTQ files.

These pipelines are actively maintained and built to scale across individual labs, institutional clusters, or cloud-based deployments. By providing structured JSON/YAML configurations, batch logging, and modular codebases, this portal empowers users to focus on biological interpretation without compromising on analytical rigor.

For a detailed breakdown of each pipeline’s steps, documentation, and usage examples, explore the dedicated pages from the navigation menu above.