categoryCompare protocols

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categoryCompare specifications

Information


Unique identifier OMICS_02122
Name categoryCompare
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.24.0
Stability Stable
Requirements
AnnotationDbi, limma, methods, KEGG.db, Biobase, utils, grDevices, R(>=2.10), affy, knitr, genefilter, GO.db, org.Hs.eg.db, annotate, GOstats, graph, hwriter, hgu95av2.db, GSEABase, estrogen, BiocGenerics(>=0.13.8), Category(>=2.33.1), colorspace, RCy3(>=1.99.29)
Maintained Yes

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categoryCompare in pipeline

2015
PMCID: 4778620
PMID: 26981369
DOI: 10.1016/j.gdata.2015.11.027

[…] particular level of radiation exposure, while a small number are shared as general radiation response biomarkers. further analysis of these genes based on categorical enrichments was performed using categorycompare (results not shown)., several genes have previously been considered as potential biomarkers for radiation exposure, including most prominently γh2afx, tp53, and cdkn1a. […]


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categoryCompare in publications

 (8)
PMCID: 5389913
PMID: 28142195
DOI: 10.1002/prot.25257

[…] (bp) gene ontology (go) annotations reported with the interproscan annotations were extracted, and the set of go terms that are direct ancestors were added to each entry using go.db v3.3.0. the categorycompare2 (v0.99.158) program was used to create annotation objects based on the set of sequences annotated and to calculate hypergeometric enrichment on the normal entries and compressed […]

PMCID: 4816878
PMID: 27077079
DOI: 10.1016/j.dib.2016.03.012

[…] 54 transcription co-factors were found to be differentially expressed, with 22 down-regulated () and 32 up-regulated ()., human entrez gene identifiers for protein homologs were used as input into categorycompare for analysis of enriched annotations including gene ontology biological process (go:bp), molecular function (go:mf) and kegg pathways . a total of 169 go:bps were enriched […]

PMCID: 4860959
PMID: 27462443
DOI: 10.1038/celldisc.2015.46

[…] the tuxedo protocol for rna-seq analysis [], parp1 depletion resulted in ~849 differentially expressed genes (degs) (p⩽0.05), of which 210 were upregulated () and 639 were downregulated (). we used categorycompare [] to determine the function of these degs (). genes upregulated after parp1 knockdown are mainly involved in nucleotide metabolism, atp synthesis and spindle (centromere) formation, […]

PMCID: 4778620
PMID: 26981369
DOI: 10.1016/j.gdata.2015.11.027

[…] particular level of radiation exposure, while a small number are shared as general radiation response biomarkers. further analysis of these genes based on categorical enrichments was performed using categorycompare (results not shown)., several genes have previously been considered as potential biomarkers for radiation exposure, including most prominently γh2afx, tp53, and cdkn1a. […]

PMCID: 4371809
PMID: 25879800
DOI: 10.1186/s12864-015-1295-9

[…] and : tables s1 – s2 for ias-mediated target genes and their corresponding transcription factors). finally, we also present a visual summary of the arsenic mediated biological processes using ‘categorycompare’ [] (figure c)., to further identify regulatory mechanisms that potentially underlie the arsenic-modulated transcript levels, we investigated whether binding sites for specific […]


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