Dataset Information

HTSvis: a web app for exploratory data analysis and visualization of arrayed high-throughput screens.

ABSTRACT:

Summary

Arrayed high-throughput screens (HTS) cover a broad range of applications using RNAi or small molecules as perturbations and specialized software packages for statistical analysis have become available. However, exploratory data analysis and integration of screening results has remained challenging due to the size of the data sets and the lack of user-friendly tools for interpretation and visualization of screening results. Here we present HTSvis, a web application to interactively visualize raw data, perform quality control and assess screening results from single to multi-channel measurements such as image-based screens. Per well aggregated raw and analyzed data of various assay types and scales can be loaded in a generic tabular format.

Availability and implementation

HTSvis is distributed as an open-source R package, downloadable from https://github.com/boutroslab/HTSvis and can also be accessed at http://htsvis.dkfz.de .

Contact

m.boutros@dkfz.de.

Supplementary information

Supplementary data are available at Bioinformatics online .

SUBMITTER: Scheeder C

PROVIDER: S-EPMC5870698 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

HTSvis: a web app for exploratory data analysis and visualization of arrayed high-throughput screens.

Scheeder Christian C Heigwer Florian F Boutros Michael M

Bioinformatics (Oxford, England) 20170901 18

<h4>Summary</h4>Arrayed high-throughput screens (HTS) cover a broad range of applications using RNAi or small molecules as perturbations and specialized software packages for statistical analysis have become available. However, exploratory data analysis and integration of screening results has remained challenging due to the size of the data sets and the lack of user-friendly tools for interpretation and visualization of screening results. Here we present HTSvis, a web application to interactive ...[more]

PMID: 28505270

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Project description:BackgroundNext-generation sequencing (NGS) has been widely used in both clinics and research. It has become the most powerful tool for diagnosing genetic disorders and investigating disease etiology through the discovery of genetic variants. Variants identified by NGS are stored in variant call format (VCF) files. However, querying and filtering VCF files are extremely difficult for researchers without programming skills. Furthermore, as the mutation data are increasing exponentially, there is an urgent need to develop tools to manage these variant data in a centralized way.MethodsThe VCF-Server was developed as a web-based visualization tool to support the interactive analysis of genetic variant data. It allows researchers and medical geneticists to manage, annotate, filter, query, and export variants in a fast and effective way.ResultsIn this study, we developed the VCF-Server, a powerful and easily accessible tool for researchers and medical geneticists to perform variant analysis. Users can query VCFs, annotate, and filter variants without knowing programming code. Once the VCF file is uploaded, VCF-Server allows users to annotate the VCF with commonly used databases or user-defined variant annotations (including variant blacklist and whitelist). Variant information in the VCF is shown visually via the interactive graphical interface. Users can filter the variants with flexible filtering rules, and the prioritized variants can be exported locally for further analysis. As VCF-Server adopts a web file system, files in the VCF-Server can be stored and managed in a centralized way. Moreover, VCF-Server allows direct web-based analysis (accessible through either desktop computers or mobile devices) as well as local deployment.ConclusionsWith an easy-to-use graphical interface, VCF-Server allows researchers with little bioinformatics background to explore and mine mutation data, which may broaden the application of NGS technology in clinics and research. The tool is freely available for use at https://www.diseasegps.org/VCF-Server?lan = eng.

Dataset Information

HTSvis: a web app for exploratory data analysis and visualization of arrayed high-throughput screens.

Summary

Availability and implementation

Contact

Supplementary information

Publications

HTSvis: a web app for exploratory data analysis and visualization of arrayed high-throughput screens.

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