More Tools Developed by Liu Lab:

Binding and Expression Target Analysis

Binding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes

Visit site »

Cistrome Chromatin Regulator

A knowledgebase on chromatin modifying enzymes and chromatin remodelers. All the chromatin regulators (CR) which possess ChIP-seq data are divided into four categories: reader, writer, eraser and remodeler. Then their basic information and their ChIP-seq data are collected and analysed.

Visit site »

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.

Visit site »

TIMER

TIMER (Tumor IMmune Estimation Resource) s a comprehensive resource for systematical analysis of immune infiltrates across diverse cancer types. The abundances of six immune infiltrates (B cells, CD4+ T cells, CD8+ T cells, Neutrphils, Macrophages and Dendritic cells) are estimated by our statistical method, which is validated using pathological estimations.

Visit site »

CARE

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.

Visit site »

TIDE

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.

Visit site »

CRISPR-FOCUS

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

Visit site »

CRISPR-DO

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.

Visit site »

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.

Visit site »

Gnosis

Gnosis is a tool for searching papers in PubMed and ranking them based on time and impact factor.

Visit site »

ChiLin

ChiLin is a short term of ChIP-seq Data Quality and Analysis Pipeline. ChiLin provides a more flexible solution for understanding the ChIP-seq analysis workflow.

Visit site »