Tools and Protocols | The Shen-Orr Lab

Tools

FIT – Found in Translation

A data-driven statistical methodology which leverages public domain gene expression data to predict from the results of a mouse experiment genes expected to be altered in the equivalent human phenotype.

Please visit the mouse2man website to use the system, and for further information.

CellAlign

High-dimensional information enables ordering of single cells based on continuous changes in measured mRNA or protein expression. CellAlign is a tool for quantitative comparison of expression dynamics within or between single-cell trajectories.

Cell Align on Github

ImmuneXpresso

immuneXpresso (iX) allows to learn about reported literature interactions between various cell types and regulatory molecules (cytokines and chemokines) these cells employ for inter-cellular signaling. Interactions captured by iX include both direct cytokine binding/secretion events and more distant, indirect influencing relations, for

example cytokines mediating cell differentiation or impacting its proliferation without

necessarily binding directly.

Please visit the ImmuneXpresso website to use the system, and for further information.

bseqsc

A bioinformatics analysis pipeline that leverages single-cell sequencing data to estimate cell type proportion and cell type-specific gene expression differences from
RNA-seq data from bulk tissue samples.

bseq-sc on Github

csSAM

csSAM is a software for deconvolution of gene expression data. It implements methods described in Shen-Orr et al. Nature Methods April 2010. csSAM is available as an R package or as a Microsoft Excel Add-in.

R package
Download the latest csSAM package (V1.2) for Windows or Source code (Mac/Unix/Linux)
csSAM Excel Add-In
Academic users: Download a copy of csSAM Excel

Commercial users: Please contact Imelda Oropeza (imelda@stanford.edu) at Stanford’s Office of Technology and Licensing for a commercial license of the csSAM Excel add-in. Please do not contact Imelda Oropeza about downloading, technical questions etc. All she handles is commercial licensing!

Protocols

Technion-Stanford joint forum for the mass cytometery community (CytoForum)
Phosphoflow protocols ols
Human Immune Monitoring Center protocols, Stanford