↓ Skip to main content

BART: bioinformatics array research tool

Overview of attention for article published in BMC Bioinformatics, August 2018
Altmetric Badge

About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (78th percentile)
  • High Attention Score compared to outputs of the same age and source (88th percentile)

Mentioned by

twitter
20 tweeters

Citations

dimensions_citation
5 Dimensions

Readers on

mendeley
24 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
BART: bioinformatics array research tool
Published in
BMC Bioinformatics, August 2018
DOI 10.1186/s12859-018-2308-x
Pubmed ID
Authors

Maria Luisa Amaral, Galina A. Erikson, Maxim N. Shokhirev

Abstract

Microarray experiments comprise more than half of all series in the Gene Expression Omnibus (GEO). However, downloading and analyzing raw or semi-processed microarray data from GEO is not intuitive and requires manual error-prone analysis and a bioinformatics background. This is due to a lack of standardization in array platform fabrication as well as the lack of a simple interactive tool for clustering, plotting, differential expression testing, and testing for functional enrichment. We introduce the Bioinformatics Array Research Tool (BART), an R Shiny web application that automates the microarray download and analysis process across diverse microarray platforms. It provides an intuitive interface, automatically downloads and parses data from GEO, suggests groupings of samples for differential expression testing, performs batch effect correction, outputs quality control plots, converts probe IDs, generates full lists of differentially expressed genes, and performs functional enrichment analysis. We show that BART enables a more comprehensive analysis of a wider range of microarray datasets on GEO by comparing it to four leading online microarray analysis tools. BART allows a scientist with no bioinformatics background to extract knowledge from their own microarray data or microarray experiments available from GEO. BART is functional on more microarray experiments and provides more comprehensive analyses than extant microarray analysis tools. BART is hosted on bart.salk.edu , includes a user tutorial, and is available for download from https://bitbucket.org/Luisa_amaral/bart .

Twitter Demographics

The data shown below were collected from the profiles of 20 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 24 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 24 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 7 29%
Researcher 5 21%
Student > Doctoral Student 3 13%
Student > Master 3 13%
Other 1 4%
Other 2 8%
Unknown 3 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 8 33%
Biochemistry, Genetics and Molecular Biology 7 29%
Computer Science 4 17%
Mathematics 1 4%
Social Sciences 1 4%
Other 0 0%
Unknown 3 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 9. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 18 August 2018.
All research outputs
#2,280,687
of 15,575,185 outputs
Outputs from BMC Bioinformatics
#889
of 5,677 outputs
Outputs of similar age
#58,359
of 278,376 outputs
Outputs of similar age from BMC Bioinformatics
#2
of 18 outputs
Altmetric has tracked 15,575,185 research outputs across all sources so far. Compared to these this one has done well and is in the 85th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 5,677 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.0. This one has done well, scoring higher than 84% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 278,376 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 78% of its contemporaries.
We're also able to compare this research output to 18 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 88% of its contemporaries.