HTSanalyzeR specifications

Information


Unique identifier OMICS_12187
Name HTSanalyzeR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.32.0
Stability Stable
Requirements
AnnotationDbi, methods, KEGG.db, snow, R(>=2.15), biomaRt, GO.db, org.Hs.eg.db, GOstats, graph, org.Mm.eg.db, org.Ce.eg.db, RankProd, igraph, GSEABase, org.Dm.eg.db, org.Rn.eg.db, BioNet, cellHTS2
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Xin Wang <>

Publication for HTSanalyzeR

HTSanalyzeR in publications

 (16)
PMCID: 5844339
PMID: 29487145
DOI: 10.1534/genetics.117.300077

[…] specifically designed for the analysis of cell-based high-throughput and high-content screens (see also ). these include, for example, the widely used bioconductor/r packages cellhts, cellhts2, and htsanalyzer for the analysis of homogeneous high-throughput assays (; ; ; ; ). cellhts, cellhts2, htsanalyzer, and web-cellhts implement all steps and utilities needed to perform quality control, […]

PMCID: 5797150
PMID: 29396566
DOI: 10.1038/s41598-018-20625-5

[…] <0.7. the metformin-protein interactome was obtained using the same methodology but excluding interactions with evidence score <0.9., pathway enrichment analysis was performed with r packages htsanalyzer for kegg to evaluate polyphenol involvement in biological pathways through their interactome. benjamini-hochberg (bh) adjusted p-values below 0.1 and pathway coverage above 10% […]

PMCID: 5699328
PMID: 29204123
DOI: 10.3389/fphys.2017.00915

[…] a given pathway, exceeds the proportion of genes that could be randomly expected (garćıa-campos et al., ). we performed ora for each module, by resorting to fdr-corrected hypergeometric tests with htsanalyzer (wang et al., ), choosing a significance below q-value = 0.001. categories larger than 1000 genes were discarded., modules were labeled according to the highest pagerank gene, i.e., […]

PMCID: 5386552
PMID: 28252645
DOI: 10.1038/cddis.2017.49

[…] represent the gene. again, p-values were adjusted for multiple testing using benjamini–hochberg correction. go analyses were carried out for each cell line separately with the bioconductor package htsanalyzer. go terms showing both a significant over-representation and enrichment were selected for further investigation. all analyses were carried out using r, and all tests were two-sided., […]

PMCID: 5296868
PMID: 28176805
DOI: 10.1038/srep41570

[…] all alignments were performed on amazon ec2 c3.8xlarge instance using a ubuntu14.04 base ami. differential gene expression was conducted using the edger package, and pathway enrichment using htsanalyzer in bioconductor., total rna was extracted from the right hemi-striatum using the rneasy lipid tissue mini kit (qiagen). tissue was homogenized in 500 μl of qiazol lysis reagent for one […]


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HTSanalyzeR institution(s)
Cancer Research UK Cambridge Research Institute, Cambridge, UK; Department of Oncology, University of Cambridge, Cambridge, UK; Cambridge Computational Biology Institute and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
HTSanalyzeR funding source(s)
The University of Cambridge, Cancer Research UK; Hutchison Whampoa Limited; Fondation Philippe Wiener - Maurice Anspach

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