Resources
Our software
CRISPR
ProTiler: An integrative pipeline for the de novo identification of essential protein domains from CRISPR/Cas9 tiling-sgRNA screens.
ProTiler-mut (coming soon). Please see our bioRxiv preprint.
GuidePro: A two-layer ensemble predictor that enables the integration of multiple factors for the prioritization of sgRNAs in protein knockouts.
A GuidePro-based web application for prioritizing sgRNAs that target protein-coding genes in human, monkey and mouse genomes is also available.
GuideVar: a transfer learning-based computational framework for the prediction of on-target efficiency and off-target effects with high-fidelity Cas9 variants.
MOFF: a a model-based predictor of Cas9-mediated off-target effects.
MoPAC: A shiny-driven application for the analysis and visualization of CRISPR/Cas9 screens on multiple samples.
MaGeCK: A model based analysis tool for identifying important genes from CRISPR/Cas9 screens.
SSC: An online tool for predicting sgRNA activity in CRISPR applications.
ChIP-seq
CCAT: A ChIP-seq analysis tool based on based on a signal-noise model (very fast!)
ChIPDiff: A Hidden-Markov Model (HMM) based application for identifying differentially modified histone sites by comparing two ChIP-seq libraries.
Genomic meta-analysis
GS2A: An analytic tool for screening genes that are associated with a set of “signature genes” from expression profiles from tumor cohorts.
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Research Areas
Find out about the four types of research taking place at UT MD Anderson.