The CellNet RNASeq Web Application available through Amazon Web Services
Legacy CellNet web application for microarray data, which has been retured from service at Harvard Medical School.
CellNet repository on Github. All training data is available under the Rpackage branch.
Amazon AWS EC2 image for RNA-Seq: CellNet_RNA-Seq_Pub ami-1ad4430d
StemSite database of regulators of the developmental origin of mouse hematopoietic stem cells.
WUHMMM (Washington University Hidden Markov Model): an algorithm for detecting DNA copy number variants from oligonucleotide array comparative genomic hybridization (aCGH) data. This package also contains an algorithm for assigning discrete CNV-region genotypes when multiple samples are available and data visualization tools. No longer updated or supported.
A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo. Stem Cell Research. 2018 Aug;31:201-215. GSE114220
Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature. 2014 Dec 4;516(7529):56-61. GSE60749
Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet. Cell. 2014 Aug 14;158(4):889-902. GSE59037
The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells. Nature Genetics. 2009 Apr;41(4):430-7. GSE10656
wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data. Nucleic Acids Research. 2008 Apr;36(7):e4. GSE10511
Education and Presentations
Software, Web Applications, and Online Databases
CellNet: network biology-based computational platform to assess establishment of cell type specific gene regulatory networks in user-provided gene expression profiles.