UpSet protocols

View UpSet computational protocol

UpSet statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Data visualization Venn diagram creation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Versioning


Add your version

Documentation


Maintainers


This tool is not maintained anymore.

Additional information


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

Publications for UpSet

UpSet in pipelines

 (5)
2018
PMCID: 5812937
PMID: 29269498
DOI: 10.1128/AEM.02294-17

[…] 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 ()., protein sequences of homologs of the z. parabailii fdh-like proteins were identified by blastp () searches against the nonredundant protein sequence database of the national […]

2018
PMCID: 5919703
PMID: 29659599
DOI: 10.1371/journal.pntd.0006438

[…] 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 […]

2017
PMCID: 5394691
PMID: 28417958
DOI: 10.1038/srep45125

[…] generated a transcript presence/absence matrix (1 = present, 0 = absent) using median cpm (counts-per-million, generated in edger) > 10 as the metric. overlaps were visualized using the r package upset. gene ontology enrichment analysis was carried out using the kolmogorov-smirnov test for significance in the r package, topgo., how to cite this article: macmanes, m. d. et al. widespread […]

2017
PMCID: 5542435
PMID: 28771474
DOI: 10.1371/journal.pbio.2002267

[…] were extracted using etetools [], and the tree topology was obtained for a given list of taxids. for tree visualization and rendering, itol [] was used, and set comparison was visualized using the upset tool []., equal amounts of an overnight culture were inoculated in 0.3% swim agar plates supplemented with appropriate additives. plates were incubated at 37°c and scanned after 4 h to 7 h. […]

2016
PMCID: 5050705
PMID: 27716060
DOI: 10.1186/s12864-016-3139-7

[…] (fc) to display differential gene expression: log2fc = log2(kd) –log2(ct); fc = 2 ^ log2fc. for combinatorial intersection analysis of ncounter datasets, we used the open source cran r package upset []., microarray analysis was performed by the duke-nus genome biology facility on an illumina platform (san diego, ca). biotin-labeled crna was prepared using the totalprep rna amplification […]


To access a full list of citations, you will need to upgrade to our premium service.

UpSet in publications

 (21)
PMCID: 5904217
PMID: 29675265
DOI: 10.1038/s41514-018-0024-4

[…] 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 […]

PMCID: 5919703
PMID: 29659599
DOI: 10.1371/journal.pntd.0006438

[…] 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 […]

PMCID: 5812937
PMID: 29269498
DOI: 10.1128/AEM.02294-17

[…] 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 ()., protein sequences of homologs of the z. parabailii fdh-like proteins were identified by blastp () searches against the nonredundant protein sequence database of the national […]

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

[…] 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 […]

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

[…] 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 []., additional file 1: table s1. additional file 2: […]


To access a full list of publications, you will need to upgrade to our premium service.

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

star_border star_border star_border star_border star_border
star star star star star

Dr Nick

star_border star_border star_border star_border star_border
star star star star star
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!