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
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.
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.
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.
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.
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.
A tool developed for high-throughput, rational sgRNA design in CRISPR screen experiment.
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.
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.
Gnosis is a tool for searching papers in PubMed and ranking them based on time and impact factor.
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.