Software and Database Resources

Cancer Immunology

  • TIMER
    "Tumor IMmune Estimation Resource, or TIMER, is a comprehensive resource for the clinical relevance of tumor-immune infiltrates, including B cells, CD4 and CD8 T cells, neutrophils, macrophages and dendritic cells."

    [Publication]
  • TRUST
    "T cell receptor Repertoire Utilities for Solid Tissue/Tumor, or TRUST is a toolbox for analyzing T cell receptors in solid tumors using unselected RNA-seq data based on de novo assembly."

    [Publication]
TIMER Results Page

CRISPR analysis

  • MAGeCK-VISPR
    Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout + Visualization of CRISPR Screens (MAGeCK-VISPR) is a comprehensive pipeline for analyzing and visualizing results from genome-scale CRISPR-Cas9 knockout screens.

    Publication submitted.
  • MAGeCK
    Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from genome-scale CRISPR-Cas9 knockout screens.

    [Publication]
VISPR Results Page
  • NEST
    Network Essentiality Scoring Tool (NEST) is designed to predict gene essentiality based on protein interaction network and gene expression. It can also be used to enhance the quality of CRISPR screen results.

    Publication submitted.

  • SSC
    Sequence Scan for CRISPR gRNA efficiency

    [Publication]
NEST Homepage

ChIP-seq and epigenetics analysis

  • RABIT
    Regression Analysis with Background Integration (RABIT) is a very efficient feature selection algorithm. We applied RABIT to find tumor associated regulators in diverse cancer types.

    [Publication]
  • Cistrome
    A web-based integrative platform for transcriptional regulation studies, from peak calling, correlation and association studies, expression analyses, to motif discovery.

    [Publication]

RABIT Results Page
  • Cistrome DB
    Collects and processes public ChIP-seq / DNase-seq data for quality control, visualization, and download.

    [Publication]
  • Model-based Analysis of ChIP-Seq (MACS)
    A model-based algorithm for finding enriched regions in ChIP-Seq experiments

    [Publication]
  • ChiLin
    ChiLin is an extensible software suite that is ideal for processing and quality control of large batches of ChIP-seq and DNase-seq data

    Publication submitted.
BETA Homepage
CEAS Example Output

Transcriptome analysis

ChIP-chip analysis

MA2C Homepage

Transcription factor motif finding

Compare Prospector Homepage