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Protocols

PRADA specifications

Information


Unique identifier OMICS_01408
Name PRADA
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Gad Getz
  • person_outline Roel Verhaak

Publication for PRADA

PRADA citations

 (14)
library_books

Genomic profiling of dedifferentiated liposarcoma compared to matched well differentiated liposarcoma reveals higher genomic complexity and a common origin

2018
PMCID: 5880260
PMID: 29610390
DOI: 10.1101/mcs.a002386

[…] To reduce false positives (), we applied an integrative analysis of multiple fusion detection methods. We first applied four tools—TopHat-Fusion (), MapSplice (), FusionMap (), and PRADA ()—to detect putative fusions in our nine pairs of frozen WD/DD samples. Then, fusions with at least one junction read and at least two supporting mate pair reads that mapped to candidate gene p […]

library_books

Novel therapeutic strategy for cervical cancer harboring FGFR3 TACC3 fusions

2018
Oncogenesis
PMCID: 5833787
PMID: 29358619
DOI: 10.1038/s41389-017-0018-2

[…] ry was about 300 bp. The adapter-ligated cDNA was amplified with 12 cycles of PCR. The samples were sequenced on the Illumina HiSeq 2500 platform with the 2 × 100-bp paired-end read module.We applied PRADA analysis to data from the above RNA sequencing experiments and obtained a list of fusion transcripts and gene expression data for each sample. […]

library_books

chimeraviz: a tool for visualizing chimeric RNA

2017
Bioinformatics
PMCID: 5870674
PMID: 28525538
DOI: 10.1093/bioinformatics/btx329

[…] Using chimeraviz, the user can import data from nine fusion-finders: deFuse (), EricScript (), InFusion (), JAFFA (), FusionCatcher (), FusionMap (), PRADA (), SOAPfuse () and STAR-FUSION (). With transcript annotation data from Ensembl and aligned RNA-sequencing data in a .BAM file, the user can create multiple visualizations of candidate fusion t […]

call_split

Characterization of fusion genes in common and rare epithelial ovarian cancer histologic subtypes

2017
Oncotarget
PMCID: 5564530
PMID: 28423358
DOI: 10.18632/oncotarget.16781
call_split See protocol

[…] Pipeline for RnAseq Data Analysis (PRADA) (v1.2) was used to call gene fusions []. Combined genome and transcriptome reference files were downloaded from http://bioinformatics.mdanderson.org/Software/PRADA/, including the hg19 assembly […]

call_split

MRI Guided Stereotactic Biopsy of Murine GBM for Spatiotemporal Molecular Genomic Assessment

2017
PMCID: 5444878
PMID: 28553660
DOI: 10.18383/j.tom.2017.00112
call_split See protocol

[…] ads of RNA-Seq data were mapped to the mouse transcriptome (GRCm38.p4/mm10) using BWA, duplicate reads were marked by Picard, and base quality scores were recalibrated using GATK, by referring to the PRADA pipeline (), followed by proceeding with the mapped reads to calculate the read counts and RPKM (reads per kilobase of transcript per million mapped reads) values for 39,017 expressed genes (Ens […]

call_split

Oncogenic function and clinical implications of SLC3A2 NRG1 fusion in invasive mucinous adenocarcinoma of the lung

2016
Oncotarget
PMCID: 5342490
PMID: 27626312
DOI: 10.18632/oncotarget.11913
call_split See protocol

[…] inks program v2.1.1 (http://cufflinks.cbcb.umd.edu/) []. Fusion-gene discovery was performed using DeFuse v0.5.0 software (http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse/) [] and PRADA v1.1 software (http://bioinformatics.mdanderson.org/main/PRADA:Overview) with default parameters. Fusion transcripts with fewer than 5 spanning reads and fewer than 3 split reads were filtered o […]


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PRADA institution(s)
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The Eli and Edythe L Broad Institute of Harvard University and MIT, Cambridge, MA, USA; Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
PRADA funding source(s)
Supported in part by NCI grant number CA143883/Chapman Foundation/Dell Foundation.

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