HTSanalyzeR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HTSanalyzeR

Tool usage distribution map

This map represents all the scientific publications referring to HTSanalyzeR per scientific context
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HTSanalyzeR specifications


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
AnnotationDbi, methods, KEGG.db, snow, R(>=2.15), biomaRt, GO.db,, GOstats, graph,,, RankProd, igraph, GSEABase,,, BioNet, cellHTS2
Maintained Yes


No version available



  • person_outline Xin Wang

Publication for HTSanalyzeR

HTSanalyzeR citations


Key Players of Cisplatin Resistance: Towards a Systems Pharmacology Approach

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 […]


RNA Interference (RNAi) Screening in Drosophila

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 […]


A computationally driven analysis of the polyphenol protein interactome

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 […]


Network Modularity in Breast Cancer Molecular Subtypes

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. […]


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

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 […]


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

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. […]

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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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