UT Southwestern Medical Center

Online Software

Software

Lung Cancer Explorer

The Lung Cancer Explorer is an online analysis tool which allows users to explore and analyze gene expression data from dozens of public lung cancer datasets online.

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Software

Pipeclip Galaxy

PIPECLIP provides a pipeline for both bioinformaticians and biologist to identify the most likely cross-linking sites from PAR-CLIP, HITS-CLIP and iCLIP sequencing data.

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Software

GRACE

Genomic Regression Analysis of Coordinated Expression website provide co-expression analysis with tumor or normal smaples from various cancer types based on TCGA studies.

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Software

Digital Pathological Image Analysis by Deep-learning

This software creates machine learning algorithms to automatically recognize pathological imaging data and correlate the automatically retrieved features with patient phenotype.

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Online Prediction Models

Model

Prognostic Model for Non Small Cell Lung Cancer

The Wang nomogram is a prognostic model for Predicting Survival in Non Small Cell Lung Cancer Patients in advanced stage on the UT Southwestern QBRC website which is a resource mainly for biomedical research.

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Model

Prognostic Model for Small Cell Lung Cancer

The Wang nomogram is a prognostic model for Predicting Survival in Small Cell Lung Cancer Patients. in advanced stage on the UT Southwestern QBRC website which is a resource mainly for biomedical research.

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Model

Drug-Induced Genomic REsponse Model (DIGREM)

DIGREM was developed to predict compound pair synergistic effect. It uses drug-treated gene expression data as input, and outputs the predicted scores of synergistic effects and rankings of drug combinations.

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Model

GeNeCK (Gene Network Construction Kit)

GeNeCK is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information.

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Software Packages

HITS-CLIP Analysis

We developed a model-based approach to detect RNA-protein binding sites in HITS-CLIP. The two-stage model, is established on all the sequencing reads to investigate binding sites at single base pair resolution. This toolbox provides essential MATLAB functions to implement our model for the identification of binding sites using heterogeneous logit models via semi-supervised learning.

PAR-CLIP HMM

The photoactivatable ribonucleoside enhanced cross-linking immunoprecipitation (PAR-CLIP) has been increasingly used for the global mapping of RNA-protein interaction sites. This package provides an integrative model to establish a joint distribution of read and mutation counts. To pinpoint the interaction sites at single base-pair resolution, we adopts non-homogeneous hidden Markov models that incorporate the nucleotide sequence.

dCLIP

dCLIP is written in Perl for discovering differential binding regions in two CLIP-Seq (HITS-CLIP or PAR-CLIP) experiments. It is appropiate in experiments where the common binding regions that are significantly enriched in both conditions tend to have similar binding strength and when researchers are more interested in the difference in binding strength rather than the binary event of whether binding site is common or not.

Bayesian Joint Analysis

Identifying which genes are differentially expressed (DE) and which gene sets are altered under two experimental conditions are both key questions in microarray analysis. Bayesian joint modeling approach to address the two key questions in parallel, which incorporates the information of functional annotations into expression data analysis and meanwhile infer the enrichment of functional groups.
Reference: Wang X, Chen M, Khodursky AB and Xiao G, Bayesian Joint Analysis of Gene Expression Data and Gene Functional Annotations, Statistics in Biosciences. 2012 Nov; 4(2): 300-318

DecoRNAi

High-throughput RNAi screening has been widely used in a spectrum of biomedical research and made it possible to study functional genomics. However, a challenge for authentic biological interpretation of large-scale siRNA or shRNA-mediated loss-of-function studies is the biological pleiotropy resulting from multiple modes of action of siRNA and shRNA reagents. A major confounding feature of these reagents is the microRNA-like translational quelling that can result from short regions (~6 nucleotides) of oligonucleotide complementarity to many different mRNAs. To help identify and correct miRNA-mimic off-target effects, we have developed DecoRNAi (deconvolution analysis of RNAi screening data) for automated quantitation and annotation of microRNA-like off-target effects in primary RNAi screening data sets. DecoRNAi can effectively identify and correct off-target effects from primary screening data and provide data visualization for study and publication. DecoRNAi contains pre-computed seed sequence families for 3 commonly employed commercial siRNA libraries. For custom collections, the tool will compute seed sequence membership from a user-supplied reagent sequence table. All parameters are tunable and output files include global data visualization, the identified seed family associations, the siRNA pools containing off-target seed families, corrected z-scores and the potential miRNAs with phenotypes of interest.

Probemapper

Connects to QBRC’s EntrezToProbe engine system to handle mappings between probes and genes and provide access to information about probes and genes.
References: Allen JD, Wang S, Chen M, Girard L, Minna J, Xie Y, Xiao G*. Probe mapping across multiple microarray platforms, Briefings in Bioinformatics, 2012 Sep;13(5):547-54. doi: 10.1093/bib/bbr076. PMID: 22199380

SbacHTS

Genome-wide RNAi screening experiments are customarily carried out on hundreds of 96-well or 384-well plates in order to study gene functions and discover novel drug targets. Spatial background noises however often blur interpretation of experimental results by distorting the distinct spatial patterns between different plates. It is therefore important to identify and correct the spatial background noises when analyzing RNAi screening data. Here, we developed an algorithm SbacHTS (Spatial background correction for High-Throughput RNAi Screening), for visualization, estimation and correction of spatial background noises of RNAi screening experiment results. SbacHTS can effectively detect and correct spatial background noise leading to higher signal/noise ratio and improved hits discovery for RNAi screening experiments. The only input required by the algorithm is the raw reads from the replicate plates.

MBCB

This package provides a model-based background correction method, which incorporates the negative control beads to pre-process Illumina BeadArray data.
References: Xie Y, Wang X, Story M. Statistical Methods of Background Correction for Illumina BeadArray. Bioinformatics, 2009, Mar 15;25(6):751-7. doi: 10.1093/bioinformatics/btp040. PMID: 19193732
Allen JD, Chen M, Xie Y (2009) Model-Based Background Correction (MBCB): R methods and GUI for Illumina Bead-array Data. J Canc Sci Ther 1: 025-027. doi:10.4172/1948-5956.1000004

Ensemble Network Aggregation (ENA)

Ensemble network aggregation is an approach which leverages the inverse-rank-product (IRP) method to combine networks. This package provides the capabilities to use IRP to bootstrap a dataset using a single method, to aggregate the networks produced by multiple methods, or to aggregate the networks produced on different datasets. Additionally, it offers convenience functions for converting between adjacency lists and matrices, and computing discrete graphs based on the Rank-Product method.