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RNA2DNAlign specifications

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Unique identifier OMICS_12823
Name RNA2DNAlign
Software type Framework/Library
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data RNA and DNA sequencing datasets
Input format VCF, BAM
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
CIRCOS, R-Studio, Integrative Genome Viewer
Maintained Yes

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Maintainer


  • person_outline Anelia Horvath

Publication for RNA2DNAlign

RNA2DNAlign citations

 (2)
library_books

Systematic pan cancer analysis of somatic allele frequency

2018
Sci Rep
PMCID: 5956099
PMID: 29769535
DOI: 10.1038/s41598-018-25462-0

[…] data commons data portal (https://portal.gdc.cancer.gov/) and processed downstream through an in-house pipeline. the rna and dna alignments, together with the variant lists were processed through rna2dnalign. rna2dnalign produced variant and reference sequencing reads counts for all the variant positions in all four datasets (normal exome, normal transcriptome, tumor exome and tumor […]

library_books

Overexpressed somatic alleles are enriched in functional elements in Breast Cancer

2017
Sci Rep
PMCID: 5557904
PMID: 28811643
DOI: 10.1038/s41598-017-08416-w

[…] therefore, the few studies that quantitatively integrate allele abundance from matching dna and rna sequencing sources are very informative., herein, we apply a software that we recently developed – rna2dnalign – to systematically quantify the allele expression of somatic variants in breast cancer samples from the cancer genome atlas (tcga). rna2dnalign counts variant and reference sequencing […]


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RNA2DNAlign institution(s)
McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington D.C., MD, USA; University of Massachusetts Medical School, Graduate School of Biomedical Sciences, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA; Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington D.C., MD, USA; Department of Computer Science, School of Engineering and applied Science, The George Washington University, Washington D.C., MD, USA; Department of Pharmacology and Physiology, The George Washington University, Washington D.C., MD, USA; Department of Mathematics, College of Engineering, Mathematics and Physical Sciences & EPSRC Centre for Predictive Modelling in Healthcare, University of Exeter, Exeter, UK
RNA2DNAlign funding source(s)
McCormick Genomic and Proteomic Center (MGPC), GWU; NIH National Center for Advancing Translational Sciences [UL1TR000075]; Clinical and Translational Science Institute at Children's National Medical Center [CTSI-CN]; Katzen Innovative Cancer Research Pilot Grant Program [RG0982]

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