Evidence map›Paper›PMID 28645171›Full record

ArticleBioinformatics (Oxford, England)2017

UpSetR: an R package for the visualization of intersecting sets and their properties.

Jake R Conway, Alexander Lex, Nils Gehlenborg

Abstract read
In one paragraph

Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2,032 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
2,032citing papers in PubMed, 2 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2,032 citing papers in PubMed, 2 syntheses or guidelines pooled it.

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1,972 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Jake R ConwayDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Alexander LexSCI Institute, School of Computing, University of Utah, Salt Lake City, UT 84112, USA.
Nils GehlenborgDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.

Funding

TrainingU54HG007963 · NHGRI · HARVARD MEDICAL SCHOOL · PI KOHANE, ISAAC S. · 2014 to 2018
$18.3M
Visual Analysis of Genomic and Clinical Data from Large Patient CohortsU01CA198935 · NCI · HARVARD MEDICAL SCHOOL · PI PARK, PETER J · 2015 to 2017
$1.5M
Visualization of (Epi)Genomic Data for Discovery of Disease-Associated VariantsR00HG007583 · NHGRI · HARVARD MEDICAL SCHOOL · PI GEHLENBORG, NILS · 2015 to 2017
$727k
NCI NIH HHS U01 CA198935NHGRI NIH HHS R00 HG007583NHGRI NIH HHS U54 HG007963
6 · The paper itself

Abstract

motivationVenn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed.

resultsWe developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. AVAILABILITY AND IMPLEMENTATION: UpSetR is available at https://github.com/hms-dbmi/UpSetR/ and released under the MIT License. A Shiny app is available at https://gehlenborglab.shinyapps.io/upsetr/ . CONTACT: nils@hms.harvard.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

SoftwareComputational BiologyGenotyping TechniquesSequence Analysis, DNA

Identifiers

PMID28645171
PMCPMC5870712

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.