Nucleic Acids Res, 2021, 49(W1):W662-W670

Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data.

Trips-Viz (https://trips.ucc.ie/) is an interactive platform for the analysis and visualization of ribosome profiling (Ribo-Seq) and shotgun RNA sequencing (RNA-seq) data. This includes publicly available and user generated data, hence Trips-Viz can be classified as a database and as a server. As a database it provides access to many processed Ribo-Seq and RNA-seq data aligned to reference transcriptomes which has been expanded considerably since its inception. Here, we focus on the server functionality of Trips-viz which also has been greatly improved. Trips-viz now enables visualisation of proteomics data from a large number of processed mass spectrometry datasets. It can be used to support translation inferred from Ribo-Seq data. Users are now able to upload a custom reference transcriptome as well as data types other than Ribo-Seq/RNA-Seq. Incorporating custom data has been streamlined with RiboGalaxy (https://ribogalaxy.ucc.ie/) integration. The other new functionality is the rapid detection of translated open reading frames (ORFs) through a simple easy to use interface. The analysis of differential expression has been also improved via integration of DESeq2 and Anota2seq in addition to a number of other improvements of existing Trips-viz features.

Kiniry SJ, Judge CE, Michel AM, Baranov PV

IBCH: 9223
Ссылка на статью в журнале: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab323/6266432
Кол-во цитирований на 03.2024: 14
Данные статьи проверены модераторами 2021-05-10

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