Chen Lab Baylor College of Medicine

Resources and Tools

Our software, tools, datasets, etc. are open-source, and free for anyone around the world to use and modify. We strive to make resources that are high quality in every aspect: cleanly written, robustly constructed and tested, well-documented, easy-to-use, accessible, customizable, and as effective as possible in real-world use.

Data portal

Human Cell Atlas

Single cell atlas of different parts of the human eye generated by combining previously published and newly generated datasets.

Mouse Cell Atlas

A unified single-cell atlas of the mouse retina using the most comprehensive approximately 323,000 single cells from our in-house experiments complementing public datasets.

Macaque Capture and Exome Database

The macaque Capture and Exome database (mCED) provides access to genotype data of rhesus macaques collected from eight non-primate research centers.

Software and Tools

bindSCBi-order Integration of multi-omics Data from Single Cell sequencing technologies

bindSC is an R package for single-cell multi-omic integration analysis. It is developed to address the challenge of single-cell multi-omic data integration that consists of unpaired cells measured with unmatched features across modalities.

MonopogenSNV calling from single-cell sequencing data

Monopogen is an analysis package for SNV calling from single-cell sequencing. Monopogen works on sequencing datasets generated from single cell RNA 10x 5’, 10x 3’, single ATAC-seq technoloiges, scDNA-seq etc.

GRIPTA novel case-control analysis method for Mendelian disease gene discovery

A novel method, the Gene Ranking, Identification and Prediction Tool (GRIPT), for performing case-control analysis of NGS data which is well-powered for disease gene discovery, especially for diseases with high locus heterogeneity.

Gulf Coast Cluster for Single Cell Omics

The GCC single cell omics cluster aims at leveraging the expertise at different institutions and maximize the interdisciplinary synergy of the group.

The eye biological network

The eye biological network will establish a comprehensive molecular and spatial atlas of the cells in the visual system across age and ethnicity groups. This resource will serve the foundation for further dissection of the function, interaction, and involvement of subtypes of cells in the visual function and diseases.
Network Coordinator: Rui Chen, Ph.D. Email

Single Cell Genomics Core

The Single Cell Genomics Core provides comprehensive services for RNA and chromatin profiling on single or a small number of cells. The core is equipped with the 10x Genomics Chromium Platform, the Takara icell8 platform, and the Fluidigm C1 auto cell prep platforms. The combination of these platforms allows cost-effective and high throughput genomic profiling that matches with the experiments.
Academic Director: Rui Chen, Ph.D. Email

X-linked Inherited Retinal Disease Variant Curation Expert Panel

We will have established variant curation rules that can be applied for all X- linked IRD genes, completed the curation of these IRD genes, and established a framework that can be modified and applied to other genes affecting inherited retinal disease.

Ancestry Network for the Human Cell Atlas of the Eye

To understand the contribution of genetic background to the human visual system, this group will generate data from diverse ancestral groups, as part of the Human Cell Atlas project.

Antibody masterlist


References:  UCSC Genome Browser   gnomAD browser   Ensembl   GeneCards   OMIM   DECIPHER   ClinGen   HGNC   NCBI   ClinVar   LOVD
Effect Predictor & others:  REVEL   CADD   EVE   dbNSFP   spliceAI   VEP   AnnotSV   Position Converter

Single Cell

Tools:  scRNA-Tools   Seurat   Cellxgene   DoubletFinder   DropletUtils   SeuratDisk   SoupX   ScPred   Scanpy   dropkick   CellRank   scvi-tools   ArchR