The Use of Transcriptomics in Clinical Applications

Borràs, Daniel; Janssen, Bart

doi:10.1002/9781119183952.ch4

Cited by 2 publications

(3 citation statements)

References 70 publications

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“…An extensive literature review was performed to define a common processing pipeline for gene expression data, detect which visual analytics approaches could be useful in that context, and define all functional requirements. During this process, no tools were found to perform all the expected steps, but many open-source libraries focusing on specific tasks were detected 2 .…”

Section: Literature Review and Definition Of Requirementsmentioning

confidence: 99%

“…One of the most developed sciences in the field is transcriptomics, which focuses on the study of the transcriptome, the sum of all the RNA transcripts of an organism [1]. Transcriptomics studies usually focus on the levels of expression of these transcripts (i.e., how many copies are found), and this information can be used to define disease biomarkers and predict risks or potential treatment responses [2].…”

Section: Introductionmentioning

confidence: 99%

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OmicSDK-Transcriptomics: A Web Platform for Transcriptomics Data Analysis

Sucre

Martínez

Garin-Muga

2023

Caring Is Sharing – Exploiting the Value in Data for Health and Innovation

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Omics sciences, especially transcriptomics, have grown exponentially since the first human genome was sequenced in 2003. Different tools have been developed in the past years for the analysis of this kind of data, but many of them require specific programming knowledge to be used. In this paper, we present omicSDK-transcriptomics, the transcriptomics module of OmicSDK, a comprehensive tool for omics data analysis that combines pre-processing, annotation and visualization tools to be used with omics data. OmicSDK comprises a command-line tool and a user-friendly web solution, so researchers having different backgrounds can take advantage of all its functionalities.

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Section: Literature Review and Definition Of Requirementsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

OmicSDK-Transcriptomics: A Web Platform for Transcriptomics Data Analysis

Sucre

Martínez

Garin-Muga

2023

Caring Is Sharing – Exploiting the Value in Data for Health and Innovation

View full text Add to dashboard Cite

show abstract

“…The transcriptome dynamically changes in response to internal and external cues; thus, it can be used as a proxy for gene-transcription activities [ 6 , 7 ], and abundance of gene end products on the bulk level under steady-state conditions [ 8 , 9 , 10 ]. With the development of numerous molecular techniques, the identification and quantification of transcriptome components has been one of the most convenient and informative avenues to understanding the molecular mechanisms of many biological processes and their regulation [ 2 , 11 ]. In particular, next-generation-sequencing (NGS) technologies have revolutionized the study of transcriptomes due to their single-base resolution, high sensitivity, high throughput, and broad dynamic range, and have dramatically decreased costs over the past decade [ 1 , 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data

Liu

et al. 2020

Genes

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Over the past decade, a large amount of RNA sequencing (RNA-seq) data were deposited in public repositories, and more are being produced at an unprecedented rate. However, there are few open source tools with point-and-click interfaces that are versatile and offer streamlined comprehensive analysis of RNA-seq datasets. To maximize the capitalization of these vast public resources and facilitate the analysis of RNA-seq data by biologists, we developed a web application called OneStopRNAseq for the one-stop analysis of RNA-seq data. OneStopRNAseq has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, such as comprehensive data-quality control, differential analysis of gene expression, exon usage, alternative splicing, transposable element expression, allele-specific gene expression quantification, and gene set enrichment analysis. Users only need to select the desired analyses and genome build, and provide a Gene Expression Omnibus (GEO) accession number or Dropbox links to sequence files, alignment files, gene-expression-count tables, or rank files with the corresponding metadata. Our pipeline facilitates the comprehensive and efficient analysis of private and public RNA-seq data.

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The Use of Transcriptomics in Clinical Applications

Cited by 2 publications

References 70 publications

OmicSDK-Transcriptomics: A Web Platform for Transcriptomics Data Analysis

OmicSDK-Transcriptomics: A Web Platform for Transcriptomics Data Analysis

OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data

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