嵌合 RNA 可视化工具
chimeraviz: a tool for visualizing chimeric RNA.
机构信息
Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
Department of Informatics, Faculty of Mathematics and Natural Sciences.
出版信息
Bioinformatics. 2017 Sep 15;33(18):2954-2956. doi: 10.1093/bioinformatics/btx329.
SUMMARY
Advances in high-throughput RNA sequencing have enabled more efficient detection of fusion transcripts, but the technology and associated software used for fusion detection from sequencing data often yield a high false discovery rate. Good prioritization of the results is important, and this can be helped by a visualization framework that automatically integrates RNA data with known genomic features. Here we present chimeraviz , a Bioconductor package that automates the creation of chimeric RNA visualizations. The package supports input from nine different fusion-finder tools: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPfuse and STAR-FUSION.
AVAILABILITY AND IMPLEMENTATION
chimeraviz is an R package available via Bioconductor ( https://bioconductor.org/packages/release/bioc/html/chimeraviz.html ) under Artistic-2.0. Source code and support is available at GitHub ( https://github.com/stianlagstad/chimeraviz ).
CONTACT
rolf.i.skotheim@rr-research.no.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
高通量 RNA 测序技术的进步使得融合转录本的检测更为高效，但用于从测序数据中检测融合的技术和相关软件通常会产生很高的假阳性率。对结果进行良好的优先级排序非常重要，这可以通过一个自动将 RNA 数据与已知基因组特征集成的可视化框架来实现。在这里，我们介绍了 chimera viz，这是一个 Bioconductor 软件包，它可以自动创建嵌合 RNA 可视化图。该软件包支持来自 9 种不同融合发现工具的输入：deFuse、EricScript、InFusion、JAFFA、FusionCatcher、FusionMap、PRADA、SOAPfuse 和 STAR-FUSION。
可用性和实现
chimeraviz 是一个可通过 Bioconductor（https://bioconductor.org/packages/release/bioc/html/chimeraviz.html）获得的 R 软件包，采用的是 Artistic-2.0 许可协议。源代码和支持可在 GitHub（https://github.com/stianlagstad/chimeraviz）上获得。
联系人
rolf.i.skotheim@rr-research.no
补充信息
补充数据可在《生物信息学》在线获取。
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