Software

Repositories

• GitHub  
• BitBucket  

Single Cell

• MAESTRO   Model-based Analyses of Transcriptome and Regulome (MAESTRO) is a comprehensive open-source computational workflow for integrative analysis of single-cell RNA-seq (scRNA-seq) and ATAC-seq (scATAC-seq) data from multiple platforms.
• MetaTiME   Meta-components in Tumor immune MicroEnvironment: MetaTiME learns data-driven, interpretable, and reproducible gene programs by integrating millions of single cells from hundreds of tumor scRNA-seq data.
• MIRA   Multimodal models for Integrated Regulatory Analysis, or MIRA, is a python package for analyzing the dynamic processes of gene regulation using single-cell multiomics datasets.

Cancer Immunotherapy

• TIMER   and TIMER2   [TIMER2 (Korea)]   [TIMER2 (China)]   Tumor IMmune Estimation Resource (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.
• TRUST   and latest version TRUST4   (tutorial video) is a computational algorithm that can extract TCR/BCR immune repertoires from tumor bulk or single cell RNA-seq data.
• DeepBCR   Deep learning framework for cancer-type classification and binding affinity estimation using B cell receptor repertoires
• TIDE   TIDE 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.
• TISMO   Tumor Immune Syngeneic MOuse (TISMO) is a database specifically designed for hosting, visualizing, and analyzing an extensive collection of syngeneic mouse model data.

Cancer Precision Medicine

• CARE   CARE is a software developed to enable large-scale inference of response biomarkers and drug combinations for targeted therapies using compound screen data.
• TIDE   TIDE 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.
• DrugCellNet   DrugCellNet is a dual-layer integrated cell line-drug network model, which uses both cell line similarity network (CSN) data and drug similarity network (DSN) data to predict the drug response of a given cell line using a weighted model.

CRISPR Analysis

• MAGeCKFlute   MAGeCKFlute is designed to support downstream analysis, utilizing the gene summary data provided through MAGeCK or MAGeCK-VISPR. Quality control, normalization, and screen hit identification for CRISPR screen data are performed in pipeline. Identified hits within the pipeline are categorized based on experimental design, and are subsequently interpreted by functional enrichment 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.
• 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.
• 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.
• CRISPR-DO   Genome-wide CRISPR gRNA design and optimization
• CRISPR-FOCUS   A tool for designing customized sgRNA libray against user input gene list.
• SSC   Sequence Scan for CRISPR gRNA efficiency.

ChIP-Seq and Epigenetics Analysis

• LISA web   command line   leverages public ChIP-seq and chromatin accessibiity profiles in CistromeDB to discover the key transcription factors and chromatin regulators from user-provided differential expression gene list.
• Cistrome-GO   Cistrome-GO is a webserver for functional enrichment analysis of transcription factor ChIP-seq peaks.
• Cistrome DB Toolkit   Backed by the huge collection of Cistrome DB, the Toolkit allows users to quickly examine their hypothesis regarding gene regulation through public ChIP-seq (protein factors and histone marks), chromatin accessibility (DNase-seq and ATAC-seq) data. Three functions have been implemented in Cistrome DB Toolkit website.
• 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.
• Cistrome   A web-based integrative platform for transcriptional regulation studies, from peak calling, correlation and association studies, expression analyses, to motif discovery.
• Cistrome DB   Collects and processes public ChIP-seq / DNase-seq data for quality control, visualization, and download.
• Model-based Analysis of ChIP-Seq (MACS)   A model-based algorithm for finding enriched regions in ChIP-Seq experiments.
• 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   Targets analysis pipeline by integration of transcriptome and ChIP-seq data.
• BINOCh   Binding Inference from Nucleosome Occupancy Changes.
• Nucleosome Positioning from Sequencing (NPS)   A signal processing-based algorithm for identifying positioned nucleosomes fromsequencing experiments at the nucleosome level.
• Cis-regulatory Element Annotation System(CEAS) - Standalone version   A standalone Python package for analyzing ChIP-chip/seq data.
• Cis-regulatory Element Annotation System(CEAS)   An integrated webserver for analyzing ChIP-chip data.

Transcriptome Analysis

• GFold   Generalized fold change for ranking differentially expressed genes from RNA-seq data.
• SAGE-seq gene EXPRESSion analysis pipelines (sageExpress)   Gene expression analysis pipelines for SAGE-Seq including tag mapping, novel normalization method using empirical Bayes and differential gene analysis.

ChIP-chip Analysis

• Model-based Analysis of Tiling-array (MAT)   A model-based algorithm for finding enriched regions in ChIP-Chip experiments.
• Model-based Analysis of 2-Color Arrays (MA2C)   A model-based algorithm for analyzing 2-color microarrays.
• extreme MApping of OligoNucleotides (xMAN)   A simple and efficient method for the mapping of millions of queryoligonucleotide fragments to the subject genome of any given length, at least an order of magnitude faster than other popular existing tools.
• Hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays (HMMTiling)   HMMTiling is a comprehensive software package for tiling array data analysis. It includes command line python applications for filtering, mapping, quantile-normalizing and enriched-region identification from ChIP-chip experiments on tiling arrays.
• Microarray Blob Remover (MBR)   A microarray JAVA tool which allows rapid visualization, detection, and removalof blob-like defects as an initial quality control step.

Transcription Factor Motif Finding

• CompareProspector   A sequence motif-finding algorithm.
• Motif Regressor   A program for finding DNA sequence motifs.
• MDscan   A fast and accurate motif finding algorithm with applications to chromatin immunoprecipitation microarray experiments.
• BioProspector   Discovering conserved DNA motifs in upstream regulatory regions of co-expressedGenes.