SetRank statistics

info info

Citations per year

info

Popular tool citations

chevron_left Gene set enrichment analysis chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

Protocols

SetRank specifications

Information


Unique identifier OMICS_16637
Name SetRank
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A gene set collection or a list of genes.
Output format CSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1.0
Stability Stable
Requirements
data.table, R.rsp, igraph, XML
Source code URL https://cran.r-project.org/src/contrib/SetRank_1.1.0.tar.gz
Maintained Yes

Download


download.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Cedric Simillion

Information


Unique identifier OMICS_16637
Name SetRank
Interface Web user interface
Input data A gene set collection or a list of genes.
Output format CSV
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable

Download


download.png

Documentation


Maintainer


This tool is not maintained anymore.

Publication for SetRank

SetRank citations

 (9)
library_books

Anti‐tumoral effects of exercise on hepatocellular carcinoma growth

2018
PMCID: 5944574
PMID: 29761175
DOI: 10.1002/hep4.1159

[…] to the classification by boyault et al. , the output of differential expression analysis for sequence count data, version 2 (deseq2) was used to perform gene set enrichment analysis (gsea) using the setrank method. the algorithm discards gene sets that have been initially flagged as significant if their significance is only due to the overlap with another gene set. it calculates the p value […]

library_books

TREM 1 promotes intestinal tumorigenesis

2017
Sci Rep
PMCID: 5665947
PMID: 29093489
DOI: 10.1038/s41598-017-14516-4

[…] and trem1 −/− tumors. gene expression values were first log-transformed. the bioconductor limma package was used to perform a moderate t-test on all genes. pathway analysis was performed using the setrank tool. the heat-map was constructed in r., all relevant data that support the findings of this study, including the full nanostring gene expression profiling data, are available […]

library_books

The hyaluronan mediated motility receptor RHAMM promotes growth, invasiveness and dissemination of colorectal cancer

2017
Oncotarget
PMCID: 5642581
PMID: 29050306
DOI: 10.18632/oncotarget.19904

[…] types and two between tumor types within expression levels. the p-values were adjusted for multiple testing using the false discovery rate approach of benjamini-hochberg as implemented in deseq2. setrank [] was used to identify gene sets enriched for differentially expressed genes. the tool collects gene sets from eight different databases (go, encode, pathway interaction database, reactome, […]

library_books

2 Deoxy D glucose Restore Glucocorticoid Sensitivity in Acute Lymphoblastic Leukemia via Modification of N Linked Glycosylation in an Oxygen Tension Independent Manner

2017
PMCID: 5549481
PMID: 28814986
DOI: 10.1155/2017/2487297

[…] of similarly regulated ions using the correlation distance as distance metric. using the silhouette width quality score, the optimal number of clusters to create was found to be 5. we then used the setrank algorithm to look for overrepresented pathways in each cluster, using metabolite annotation from the kegg and reactome databases [, ]., reh and sd1 leukemia cells were screened with a library […]

library_books

Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver

2017
Sci Rep
PMCID: 5527063
PMID: 28743867
DOI: 10.1038/s41598-017-06634-w

[…] applied science, penzberg, germany) using the following program: 95 °c for 10 min; 45 cycles of 95 °c for 10 s, 60 °c for 10 s, and 72 °c for 10 s; 72 °c for 6 min., we used the kobas software and setrank for the gene ontology (go) enrichment and kyoto encyclopedia of genes and genomes (kegg) pathway analyses of the differentially expressed genes (degs) and predicted target genes […]

library_books

PIF* promotes brain re myelination locally while regulating systemic inflammation clinically relevant multiple sclerosis M.smegmatis model

2017
Oncotarget
PMCID: 5400627
PMID: 28423529
DOI: 10.18632/oncotarget.15662

[…] graphpad prism 5.03 (graphpad software, inc. la jolla, usa); p<0.05 was considered significant. the output of the limma analysis was used to perform gene set enrichment analysis (gsea) using the setrank method. the key principle of this algorithm is that it discards gene sets that have initially been flagged as significant, if their significance is only due to the overlap with another gene […]


Want to access the full list of citations?
SetRank institution(s)
Interfaculty Bioinformatics Unit and SIB Swiss Institute of Bioinformatics, University of Bern, Berne, Switzerland; Department of Clinical Research, University of Bern, Berne, Switzerland; Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; SIB Technology, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
SetRank funding source(s)
Supported by the University of Bern and the Directorate of Teaching and Research of the Insel Gruppe Bern.

SetRank reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SetRank