Article ; Online: SPOT: a web-tool enabling swift profiling of transcriptomes.
Bioinformatics (Oxford, England)
2021 Volume 38, Issue 1, Page(s) 284–285
Abstract: ... shinyapps.io/SPOT/ and https://github.com/EliasFarr/SPOT.: Supplementary information: Supplementary data ...
| Abstract | The increasing number of single cell and bulk RNAseq datasets describing complex gene expression profiles in different organisms, organs or cell types calls for an intuitive tool allowing rapid comparative analysis. Here, we present Swift Profiling Of Transcriptomes (SPOT) as a web tool that allows not only differential expression analysis but also fast ranking of genes fitting transcription profiles of interest. Based on a heuristic approach the spot algorithm ranks the genes according to their proximity to the user-defined gene expression profile of interest. The best hits are visualized as a table, bar chart or dot plot and can be exported as an Excel file. While the tool is generally applicable, we tested it on RNAseq data from malaria parasites that undergo multiple stage transformations during their complex life cycle as well as on data from multiple human organs during development and cell lines infected by SARS-CoV-2. SPOT should enable non-bioinformaticians to easily analyse their own and any available dataset. Availability and implementation: SPOT is freely available for (academic) use at: https://frischknechtlab.shinyapps.io/SPOT/ and https://github.com/EliasFarr/SPOT. Supplementary information: Supplementary data are available at Bioinformatics online. |
|---|---|
| MeSH term(s) | Humans ; Software ; Transcriptome ; COVID-19 ; SARS-CoV-2 ; Algorithms |
| Language | English |
| Publishing date | 2021-07-20 |
| Publishing country | England |
| Document type | Journal Article ; Research Support, Non-U.S. Gov't |
| ZDB-ID | 1422668-6 |
| ISSN | 1367-4811 ; 1367-4803 |
| ISSN (online) | 1367-4811 |
| ISSN | 1367-4803 |
| DOI | 10.1093/bioinformatics/btab541 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
More links
Kategorien
In stock of ZB MED Cologne/Königswinter
| Zs.A 2374: Show issues | Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG) |
Order via subito
This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.