HTSanalyzeR statistics

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Protocols

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


No version available

Documentation


Maintainer


  • person_outline Xin Wang

Publication for HTSanalyzeR

HTSanalyzeR citations

 (19)
library_books

Key Players of Cisplatin Resistance: Towards a Systems Pharmacology Approach

2018
Int J Mol Sci
PMCID: 5877628
PMID: 29518977
DOI: 10.3390/ijms19030767

[…] After the identification of differentially expressed genes, a Gene Set Enrichment Analysis (GSEA) [] was performed with respect to Gene Ontology (GO) terms [] using HTSanalyzeR []. GSEA is a widely used method comparing the mapping of genes to a defined GO term with a ranking of these genes, e.g., via logarithmic fold change. The GSEA method calculates a score as […]

library_books

RNA Interference (RNAi) Screening in Drosophila

2018
Genetics
PMCID: 5844339
PMID: 29487145
DOI: 10.1534/genetics.117.300077

[…] e 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, norm […]

library_books

A computationally driven analysis of the polyphenol protein interactome

2018
Sci Rep
PMCID: 5797150
PMID: 29396566
DOI: 10.1038/s41598-018-20625-5

[…] 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% were consid […]

library_books

Network Modularity in Breast Cancer Molecular Subtypes

2017
Front Physiol
PMCID: 5699328
PMID: 29204123
DOI: 10.3389/fphys.2017.00915

[…] in 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. […]

call_split

Neuroblastoma cells depend on HDAC11 for mitotic cell cycle progression and survival

2017
PMCID: 5386552
PMID: 28252645
DOI: 10.1038/cddis.2017.49
call_split See protocol

[…] to 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.Effects […]

library_books

Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.HttQ111/+ model of Huntington’s disease

2017
Sci Rep
PMCID: 5296868
PMID: 28176805
DOI: 10.1038/srep41570

[…] ignment. 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. […]

Citations

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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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