<commit_before>---
layout: page
title: "Resources"
subheadline: "Softwares and Databses"
meta_title: "Resources for Research Use - Verhaak Lab"
meta_description: "Softwares, databases and other resources in cancer computational biology by Verhaak Lab"
permalink: "/resources/"
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---

#### <i class="fa fa-users"></i> [Looking for available positions ?]({{ site.url }}/positions)


## <i class="fa fa-cubes"></i> Tools:
***

### [PRADA](http://bioinformatics.mdanderson.org/main/PRADA:Overview)

Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. The BAM files generated by the pipeline are readily compatible with different tools for mutation calling and to obtain read counts for further downstream analysis.

>Publication: <NAME>, <NAME>, .., Verhaak RG. PRADA: pipeline for RNA sequencing data analysis. *Bioinformatics* 2014. PMID: [24695405](http://www.ncbi.nlm.nih.gov/pubmed/24695405)

### [ESTIMATE](http://bioinformatics.mdanderson.org/main/ESTIMATE:Overview)

ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data) is a tool for predicting tumor purity, and the presence of infiltrating stromal/immune cells in tumor tissues using gene expression data. ESTIMATE algorithm is based on single sample Gene Set Enrichment Analysis and generates three scores:

1. Stromal score (that captures the presence of stroma in tumor tissue)
2. Immune score (that represents the infiltration of immune cells in tumor tissue), and 
3. Estimate score (that infers tumor purity). 

The [website](http://ibl.mdanderson.org/estimate/) presents the scores for all TCGA tumor types.

>Publication: <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>,   <NAME>,  <NAME>, Verhaak R. Inferring tumour purity and stromal and immune cell admixture from expression data. *Nature Communications* 2013. PMID: [2411377](http://www.ncbi.nlm.nih.gov/pubmed/24113773)

## <i class="fa fa-database"></i> Database:
***

### [TumorFusions](http://tumorfusions.org)

Transcripts fusion as a result of genomic rearrangement is an important class of somatic alteration, as a cancer initiating event and as a molecular therapeutic target for specific tumors. Our Pipeline for RNA sequencing Data Analysis (PRADA) enables us to detect fusion transcripts with high confidence comprehensively. Based on integrated analysis of paired-end RNA sequencing and DNA copy number data from The Cancer Genome Atlas(TCGA), TCGA Fusion Gene Data Portal provides a bona-fide fusion list across many tumor types.

>Publication: Yoshihara, K. <NAME>, .., Verhaak RG. The landscape and therapeutic relevance of cancer-associated transcript fusions. Oncogene. 2014. PMID: [25500544](http://www.ncbi.nlm.nih.gov/pubmed/25500544)<commit_msg>Update resources.md<commit_after>---
layout: page
title: "Resources"
subheadline: "Softwares and Databses"
meta_title: "Resources for Research Use - Verhaak Lab"
meta_description: "Softwares, databases and other resources in cancer computational biology by Verhaak Lab"
permalink: "/resources/"
comments: false
show_meta: false
---

#### <i class="fa fa-users"></i> [Looking for available positions ?]({{ site.url }}/positions)


## <i class="fa fa-cubes"></i> Tools:
***

### [PRADA](http://bioinformatics.mdanderson.org/main/PRADA:Overview)

Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. The BAM files generated by the pipeline are readily compatible with different tools for mutation calling and to obtain read counts for further downstream analysis.

>Publication: <NAME>, <NAME>, .., Verhaak RG. PRADA: pipeline for RNA sequencing data analysis. *Bioinformatics* 2014. PMID: [24695405](http://www.ncbi.nlm.nih.gov/pubmed/24695405)

### [ESTIMATE](http://bioinformatics.mdanderson.org/main/ESTIMATE:Overview)

ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data) is a tool for predicting tumor purity, and the presence of infiltrating stromal/immune cells in tumor tissues using gene expression data. ESTIMATE algorithm is based on single sample Gene Set Enrichment Analysis and generates three scores:

1. Stromal score (that captures the presence of stroma in tumor tissue)
2. Immune score (that represents the infiltration of immune cells in tumor tissue), and 
3. Estimate score (that infers tumor purity). 

The [website](http://ibl.mdanderson.org/estimate/) presents the scores for all TCGA tumor types.

>Publication: <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>,   <NAME>,  <NAME>, <NAME>. Inferring tumour purity and stromal and immune cell admixture from expression data. *Nature Communications* 2013. PMID: [2411377](http://www.ncbi.nlm.nih.gov/pubmed/24113773)

## <i class="fa fa-database"></i> Database:
***

### [TumorFusions.Org](http://tumorfusions.org)

Transcripts fusion as a result of genomic rearrangement is an important class of somatic alteration, as a cancer initiating event and as a molecular therapeutic target for specific tumors. Our Pipeline for RNA sequencing Data Analysis (PRADA) enables us to detect fusion transcripts with high confidence comprehensively. Based on integrated analysis of paired-end RNA sequencing and DNA copy number data from The Cancer Genome Atlas(TCGA), TCGA Fusion Gene Data Portal provides a bona-fide fusion list across many tumor types.

>Publication: Yoshihara, <NAME>, .., Verhaak RG. The landscape and therapeutic relevance of cancer-associated transcript fusions. Oncogene. 2014. PMID: [25500544](http://www.ncbi.nlm.nih.gov/pubmed/25500544)
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