Web Resources

KmerKeys

A web resource for searching indexed genome assemblies and variants via exact and fuzzy K-mer sequences.

HEMnet – Hematoxylin & Eosin and Molecular neural network

A deep learning automated cancer diagnosis software using molecular labeling to improve the pathological annotation of Hematoxylin and Eosin (H&E) stained tissue.

The Cancer Genome Atlas Clinical Explorer

The NIH Cancer Genome Atlas (TCGA) project has generated enormous data sets covering > 20 malignancies and provides many valuable insights into the underlying genetic and genomic basis of cancer. However, exploring the association between TCGA results and clinical phenotype remains a challenge, particularly for individuals lacking formal bioinformatics training.

MendeLIMS Demo

An open source web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation sequencing technologies.

Oligo Exome Project

Stanford Human OligoExome is a scalable oligonucleotide management system for genomic analysis and high-throughput resequencing. This set of capture oligonucleotides will cover the CCDS exon space and a high proportion of related regulatory regions from the human genome.

Oligo Genome Project

The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011.