SetRank protocols

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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

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Versioning


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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


Documentation


Maintainer


This tool is not maintained anymore.

Publication for SetRank

SetRank in pipeline

2017
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, […]


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SetRank in publications

 (9)
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 […]

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 […]

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, […]

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 […]

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 […]


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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.

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