HTSCluster statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


HTSCluster specifications


Unique identifier OMICS_07338
Name HTSCluster
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 2.0.8
Stability Stable
stats, graphics, Biobase, grDevices, edgeR, plotrix, R(≥2.10.0), capushe, HTSFilter
Maintained Yes


No version available



  • person_outline Andrea Rau

Publication for HTSCluster

HTSCluster citations


Proanthocyanidin accumulation and transcriptional responses in the seed coat of cranberry beans (Phaseolus vulgaris L.) with different susceptibility to postharvest darkening

BMC Plant Biol
PMCID: 5445279
PMID: 28545577
DOI: 10.1186/s12870-017-1037-z
call_split See protocol

[…] raw read counts for all differentially expressed genes were obtained from Binary Alignment/Map (BAM) files using samtools [] v0.1.17 and HTSeq v0.6.1p2 []. Clustering of genes was performed with the HTSCluster v2.0 package [] in R [] with the number of clusters ranging from 1 to 50. A model containing 14 clusters was selected a posteriori using the model selection criterion Dimension jump []. The […]


Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

BMC Genomics
PMCID: 5359931
PMID: 28320315
DOI: 10.1186/s12864-017-3623-8

[…] r heatmap representations.Transcripts with estimated expression values ≤0.01 were removed prior to clustering. To cluster sets of co-expressed genes within each species, we performed clustering using HTSCluster []. Unlike other commonly used clustering algorithms (e.g., k-means, hierarchical), HTSCluster is a model based clustering approach that uses Poisson mixture models to cluster sequences usi […]


Under Expression of Chemosensory Genes in Domiciliary Bugs of the Chagas Disease Vector Triatoma brasiliensis

PLoS Negl Trop Dis
PMCID: 5085048
PMID: 27792774
DOI: 10.1371/journal.pntd.0005067

[…] differential expression analysis software with this kind of data is ongoing.Recently, a gene clustering methodology based on transcriptomic data has been developed to highlight co-expressed contigs (HTSCluster, []). We found similar results using differential expression analysis and the HTSCluster gene clustering methodology. Furthermore, gene clustering provides additional detail about the dynam […]


Extensive localization of long noncoding RNAs to the cytosol and mono and polyribosomal complexes

Genome Biol
PMCID: 4053777
PMID: 24393600
DOI: 10.1186/gb-2014-15-1-r6
call_split See protocol

[…] Subsequently, normalization was performed using the DEseq [] to correct for library size and technical biases. Gene clustering was performed using a model-based clustering approach with the R package HTSCluster []. The protein coding-lncRNA correlation matrix (Figure ) was calculated using Spearman rank correlation. The matrix was visualized after hierarchical clustering using Euclidean distance w […]


Looking to check out a full list of citations?

HTSCluster institution(s)
INRA, UMR1313 Génétique animale et biologie intégrative, Jouy-en-Josas, France, AgroParisTech, UMR1313 Génétique animale et biologie intégrative, Paris 05, France; Institut de Mathématiques de Toulouse, INSA de Toulouse, Université de Toulouse, Toulouse, France; UMR AgroParisTech/INRA MIA 518, Paris, France; INRA, UMR 1165 URGV, Saclay Plant Sciences, Evry, France; UEVE, UMR URGV, Saclay Plant Sciences, Evry, France; CNRS, ERL 8196, URGV, Saclay Plant Sciences, Evry, France; Inria Saclay - Île-de-France, Orsay, France

HTSCluster reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review HTSCluster