UpSet statistics

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Citations per year

Number of citations per year for the bioinformatics software tool UpSet
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Tool usage distribution map

This map represents all the scientific publications referring to UpSet per scientific context
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Associated diseases

This word cloud represents UpSet usage per disease context
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Popular tool citations

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Protocols

UpSet specifications

Information


Unique identifier OMICS_16309
Name UpSet
Alternative name UpSetR
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input format CSV
License MIT License
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Alexander Lex
  • person_outline Nils Gehlenborg
  • person_outline Jake Conway

Additional information


https://gehlenborglab.shinyapps.io/upsetr/

Information


Unique identifier OMICS_16309
Name UpSet
Alternative name UpSetR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A table in which the rows represent elements and columns include set assignments and additional attributes, Sets of elements names; An expression describing the size of the set intersections as introduced by the venneuler package.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Version 1.3.3
Stability Stable
Source code URL https://cran.r-project.org/src/contrib/UpSetR_1.3.3.tar.gz
Registration required Yes

Download


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Versioning


No version available

Documentation


Maintainers


This tool is not maintained anymore.

Additional information


https://gehlenborglab.shinyapps.io/upsetr/

Publications for UpSet

UpSet citations

 (21)
call_split

Tissue specific transcriptome profiling of Drosophila reveals roles for GATA transcription factors in longevity by dietary restriction

2018
PMCID: 5904217
PMID: 29675265
DOI: 10.1038/s41514-018-0024-4
call_split See protocol

[…] tmap.2 function from the gplots library, either on fold-changes calculated by DESeq2, or median of variance-stabilised GATA TF expression. Intersections between DE gene sets were visualised using the upset library.Fly survival and egg laying data were analysed in R (v3.1.1). Survival data were analysed using the coxph function from the survival library. Egg laying data were normalised to number of […]

call_split

Profiling extracellular vesicle release by the filarial nematode Brugia malayi reveals sex specific differences in cargo and a sensitivity to ivermectin

2018
PLoS Negl Trop Dis
PMCID: 5919703
PMID: 29659599
DOI: 10.1371/journal.pntd.0006438
call_split See protocol

[…] nt list from which mammalian contaminants were subtracted. Data were filtered using 1% protein and peptide FDR and requiring at least two unique peptides per protein. Protein sets were compared using UpSetR (40), a novel web-based technique to analyze discrete data sets and their intersections. GO analysis was performed using Blast2GO v.4 (BioBam Bioinformatics, Valencia, Spain), a program that ex […]

library_books

Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii

2018
Appl Environ Microbiol
PMCID: 5812937
PMID: 29269498
DOI: 10.1128/AEM.02294-17

[…] ied to the three sets of upregulated genes (18 h, 42 h, and both time points) as well as to the corresponding three sets of downregulated genes (Data Set S6). The output of goseq was visualized using UpsetR v.1.3.3 (). […]

library_books

Comparison of genomes and proteomes of four whole genome sequenced Campylobacter jejuni from different phylogenetic backgrounds

2018
PLoS One
PMCID: 5749857
PMID: 29293692
DOI: 10.1371/journal.pone.0190836

[…] ance measure with heatmap.2 function in R, and PCA was conducted using prcomp with variable zero-centered and scaled to have unit variance. Differential expressed protein counts were visualized using UpSet plots [] generated with the UpSetR package [] in R. GI numbers of identified proteins were converted to Uniprot ID using Retrieve/ID mapping (http://www.uniprot.org/uploadlists/), and GO enrichm […]

library_books

Transcriptional effects of a positive feedback circuit in Drosophila melanogaster

2017
BMC Genomics
PMCID: 5746007
PMID: 29281970
DOI: 10.1186/s12864-017-4385-z

[…] values assigned to a single Ensembl Gene ID, we retained only the probe with the lowest p value.Common gene sets diagrams, principal component analysis, and genomic plots were generated using limma, UpSetR [] prcomp and Bioconductor [] packages. Sliding window analysis was run using a custom function. Plots and diagrams were made with ggplot2 []. […]

library_books

Systems analysis identifies melanoma enriched pro oncogenic networks controlled by the RNA binding protein CELF1

2017
Nat Commun
PMCID: 5740069
PMID: 29269732
DOI: 10.1038/s41467-017-02353-y

[…] n the Venn diagrams of Fig. ). These CELF1-bound transcripts in melanoma were merged with the five available genome-wide analyses for CELF1 in human cancer cells described above. As summarized in the UpSet plot of Fig.  (see figure legend for explanation), the overlap with the different data sets of HeLa, T cells, K562, and GM12878 was very low, with no common targets to all these cell lines (see […]


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UpSet institution(s)
Harvard University, Cambridge, MA, USA
UpSet funding source(s)
This work was supported in part by the Austrian Science Fund (J 3437-N15), the Air Force Research Laboratory and DARPA grant FA8750-12-C-0300 and the United States National Institutes of Health (K99 HG007583).

UpSet review

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Dr Nick

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Web
An amazing tool that has revolutionized how I present comparative datasets! The usefulness of Venn diagrams breaks down past three comparisons. This makes numerous cross comparisons immensely clear and adds a plethora of additional information. The web version is nice for a quick and dirty graphic, but I like the flexibility the R version offers. My only qualm is that there is not (or else I've not yet discovered) an option to prioritize a single or group of sets such that I only see intersections with that one or those subsets. Modifying the input matrix, such that the set of interest is essentially a baseline, is a potential solution, but I would prefer a built-in function for that task that preserves the size of the sets against which I am comparing. Otherwise, this is a must use tool!