BDB Genomics develops "open-source" computational infrastructure for epigenomic data analysis, with a focus on reproducibility, accessibility, and scalable design.
Type 2 Diabetes epigenomics.
Cancer
BigDataBiology Genomics | Computational Epigenomics
Engineering open-source epigenomics infrastructure for disease biology.
Popular repositories Loading
-
bdb-atacseq
bdb-atacseq PublicA production-grade, modular Snakemake framework for reproducible ATAC-seq analysis, featuring upfront configuration validation and robust QC gating.
Python 2
-
bdb-rnaseq
bdb-rnaseq PublicProduction-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
-
scchromatinR
scchromatinR PublicA lightweight R package that infers chromatin remodelling velocity from scATAC-seq data
R 1
-
bdb-cutandrun
bdb-cutandrun PublicA 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
-
-
AlphaGenomeR
AlphaGenomeR PublicR interface to Google DeepMind AlphaGenome API. Bridging gRPC-based multimodal genomic predictions (RNA-seq, ATAC, Splicing, 3D Genome) into R-native workflows.
R
Repositories
Showing 10 of 12 repositories
- bdb-atacseq Public
A production-grade, modular Snakemake framework for reproducible ATAC-seq analysis, featuring upfront configuration validation and robust QC gating.
- 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. Designed following ENCODE and nf-core best practices.
- 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 normalization, and MultiQC reporting. HPC-ready with Singularity support.
- rna-seq-reanalysis Public
- .github Public
- scchromatinR Public
A lightweight R package that infers chromatin remodelling velocity from scATAC-seq data
- EvoR Public
R interface to Evo 2 via NVIDIA BioNeMo. Enabling zero-shot variant effect prediction and generative genomics in R-native workflows.
- 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.
- ligateR Public
Takes a list of genes and builds one graph connecting them, using data from KEGG, STRING, Gene Ontology, UniProt, Ensembl, and Reactome. Matches gene names across these databases, notes which database each connection came from, and records which version of each database was used so results can be reproduced later.
- bdb-sample-registry Public
A centralized PostgreSQL database to store and manage sample metadata across all BDB Genomics epigenomic pipeline assays with integrated QC tracking to flag and monitor low-quality samples.
People
This organization has no public members. You must be a member to see who’s a part of this organization.
Top languages
Loading…
Most used topics
Loading…