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AnnBuilder specifications

Information


Unique identifier OMICS_15640
Name AnnBuilder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format XML
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.14.0
Stability Stable
Requirements
methods, Biobase, XML, annotate, utils
Maintained Yes

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Maintainer


  • person_outline Jianhua Zhang <>

Publication for AnnBuilder

AnnBuilder in publications

 (12)
PMCID: 3277307
PMID: 22095690
DOI: 10.1093/hmg/ddr536

[…] term or kegg pathway occurs more frequently in the set of genes than it would be expected based on the frequency of its occurrence in the entire chip. the chip spotted transcripts were annotated by annbuilder package for getting go terms, and by kegg package and custom software written in perl and r for pathway annotation. to evaluate which pathways or functional categories were enriched in ald […]

PMCID: 3001492
PMID: 21179454
DOI: 10.1371/journal.pone.0015504

[…] series. array probe annotations used in the analyses described in this manuscript were a merge of those obtained from the geisha resource website and a custom annotation package compiled using r/annbuilder package., p19cl6 cells expressing green fluorescent protein (gfp) under the transcriptional control of the 250 bp mlc-2v promoter , a kind gift from christine mummery, were cultured […]

PMCID: 3091682
PMID: 20920310
DOI: 10.1186/1471-2164-11-533

[…] the false discovery rate (fdr), which is the standard setting in bingo 2.3 [], was controlled., the statistical programming software r 2.7.1 was used in combination with bioconductor [,] packages annbuilder 1.18.0, kegg.db version 2.2.0, and gostats version 1.7.4 to acquire a list of pathways that were associated with one or more of the 246 host gene proteins., strategies to perform […]

PMCID: 2785841
PMID: 19925670
DOI: 10.1186/1471-2164-10-544

[…] and 2) a unigene identifier, which was used to map the features on the array, and an annotation package, which was built using the bioconductor package annbuilder (version 1.14.0)., in step 6, each gene on the array was assigned to a go identifier, and a gene set enrichment test was performed to compare p&r vs. p and r vs. p using limma [,]. […]

PMCID: 2535776
PMID: 18684314
DOI: 10.1186/1746-6148-4-29

[…] be ignored. the top 1% of the genes was considered for further analyses. the array features were mapped to a locuslink identifier and an annotation package was built using the bioconductor package annbuilder (version 1.9.14). go terms (p < 0.01 and more than 10 significant genes) were analysed for overrepresentation using the gohyperg function of the bioconductor package gostats (version […]


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AnnBuilder institution(s)
Department of Biostatistical Science, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA; Channing Laboratory, Boston, MA, USA
AnnBuilder funding source(s)
This work was supported by the High Tech Industry Multidisciplinary Research Fund at the Dana-Farber Cancer Institute.

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