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@BDB-Genomics

BigDataBiology Genomics | Computational Epigenomics

Engineering open-source epigenomics infrastructure for disease biology.
README.md
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BigDataBiology Genomics | Computational Epigenomics

BDB Genomics develops "open-source" computational infrastructure for epigenomic data analysis, with a focus on reproducibility, accessibility, and scalable design.

Research Focus

Metabolic Diseases, Metabolic Oncology, and Infectious Diseases

Support

"His project addresses a well-recognised barrier in global health research that requires urgent development... Working pipelines for ATAC-seq, ChIP-seq, and CUT&RUN are already publicly available at BDB-Genomics and built to production best practices... We believe this project represents a meaningful contribution to research capacity building in global health, and we are glad to support and follow Mr Bhandary's efforts."

— Dr. Gemma Langridge, JIDCuk Charitable Trust

Popular repositories Loading

  1. bdb-atacseq bdb-atacseq Public

    A production-grade, modular Snakemake framework for reproducible ATAC-seq analysis, featuring upfront configuration validation and robust QC gating.

    Python 2

  2. bdb-rnaseq bdb-rnaseq Public

    Production-grade, modular Snakemake pipeline for RNA-seq analysis. Includes QC (FastQC, fastp), alignment (STAR), quantification (featureCounts), post-alignment QC (RSeQC, Preseq, Picard), DESeq2 …

    Python 2

  3. scchromatinR scchromatinR Public

    A lightweight R package that infers chromatin remodelling velocity from scATAC-seq data

    R 1

  4. bdb-cutandrun bdb-cutandrun Public

    A modular, production-ready Snakemake pipeline for CUT&RUN epigenomic analysis — featuring E. coli spike-in normalization, SEACR peak calling, fragment size analysis, and comprehensive QC reporting…

    Python

  5. .github .github Public

  6. AlphaGenomeR AlphaGenomeR Public

    R interface to Google DeepMind AlphaGenome API. Bridging gRPC-based multimodal genomic predictions (RNA-seq, ATAC, Splicing, 3D Genome) into R-native workflows.

    R

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