Details

Autor(en) / Beteiligte

• Castillo-Lara, S
• Pascual-Carreras, E
• Abril, J F
• Wren, Jonathan

Titel

PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resources

Ist Teil von

• Bioinformatics, 2020-03, Vol.36 (6), p.1889-1895

Ort / Verlag

England: Oxford University Press

Erscheinungsjahr

2020

Quelle

EZB Electronic Journals Library

Beschreibungen/Notizen

• Abstract Motivation There is an increasing amount of transcriptomic and genomic data available for planarians with the advent of both traditional and single-cell RNA sequencing technologies. Therefore, exploring, visualizing and making sense of all these data in order to understand planarian regeneration and development can be challenging. Results In this work, we present PlanExp, a web-application to explore and visualize gene expression data from different RNA-seq experiments (both traditional and single-cell RNA-seq) for the planaria Schmidtea mediterranea. PlanExp provides tools for creating different interactive plots, such as heatmaps, scatterplots, etc. and links them with the current sequence annotations both at the genome and the transcript level thanks to its integration with the PlanNET web application. PlanExp also provides a full gene/protein network editor, a prediction of genetic interactions from single-cell RNA-seq data, and a network expression mapper that will help researchers to close the gap between systems biology and planarian regeneration. Availability and implementation PlanExp is freely available at https://compgen.bio.ub.edu/PlanNET/planexp. The source code is available at https://compgen.bio.ub.edu/PlanNET/downloads. Supplementary information Supplementary data are available at Bioinformatics online.