More Tools Developed by Liu Lab:



TIDE (Tumor Immune Dysfunction and Exclusion) is a gene expression biomarker to predict the clinical response to immune checkpoint blockade.TIDE also provides gene-wise associations with T-cell dysfunction and immunotherapy resistance, computed from a large amount of cancer genomics datasets.

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TIMER2 (Tumor IMmune Estimation Resource) provides comprehensive analysis and visualization functions of tumor infiltrating immune cells. It provides interfaces for investigating the associations between immune infiltrates and genetic or clinical features, and for exploring cancer-related associations in the TCGA cohorts.

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TISMO (Tumor Immune Syngeneic MOuse) is a database specifically designed for hosting, visualizing, and analyzing an extensive collection of syngeneic mouse model data. It provides interactive interfaces for users to explore gene expression and immune infiltration, and allows systematic comparisons between different model characteristics, and treatment and response groups.

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CRISPR tools

Sequence Scan for CRISPR

A new sequence model for predicting sgRNA efficiency for CRISPR knockout or CRISPRi/a by systematically assessing the DNA sequence features that contribute to single guide RNA (sgRNA) efficiency in CRISPR-based screens.

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This application focus on the whole genome sgRNA design in human and mouse, with accessing both the efficiency and the specificity score. It also have the epigenome browser as a visualization tool for users to identify each of the sgRNA with genome features overlapping like DHS, SNP.

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A tool developed for high-throughput, rational sgRNA design in CRISPR screen experiment.

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Cistrome CR

Cistrome CR is a a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse. It provides ChIP-Seq analysis data for the targeted histone modifications and schematized the relationships between them.

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Nuclear Receptor Cistrome DB

A curated database of 88 nuclear receptor cistrome data sets and other associated high-throughput data sets including 121 collaborating factor cistromes, 94 epigenomes, and 319 transcriptomes. All the ChIP_chip/seq peak regions are annotated with enriched HRE and co-regulator motifs. A list of predicted hormone response genes from integration of nuclear receptor ChIP_chip/seq data and differential expression data is also readily available to the users.

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CARE (Computational Analysis of REsistance) is a software developed to enable large-scale inference of response biomarkers and drug combinations for targeted therapies using compound screen data.

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