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Protocols

HTSCluster specifications

Information


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
Requirements
stats, graphics, Biobase, grDevices, edgeR, plotrix, R(≥2.10.0), capushe, HTSFilter
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Andrea Rau

Publication for HTSCluster

HTSCluster citations

 (4)
call_split

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

2017
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 […]

library_books

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

2017
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 […]

library_books

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

2016
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 […]

call_split

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

2014
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 […]

Citations

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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

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