HTSCluster statistics

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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

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Documentation


Maintainer


  • person_outline Andrea Rau <>

Publication for HTSCluster

HTSCluster in pipelines

 (2)
2017
PMCID: 5359931
PMID: 28320315
DOI: 10.1186/s12864-017-3623-8

[…] 93.39%, 95.1%, and 92.07%, respectively. additionally, mapping reads from one species onto another species reference produced successful mapping rates of >85%., over 5 independent runs, we used htscluster [] and the em algorithm [] to fit a sequence of poisson mixture models with k = 1, 2, …, 60 clusters for the expression estimates of each reference transcriptome. using slope heuristics […]

2017
PMCID: 5359931
PMID: 28320315
DOI: 10.1186/s12864-017-3623-8

[…] 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 […]


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HTSCluster in publications

 (6)
PMCID: 5796731
PMID: 29360820
DOI: 10.1371/journal.pgen.1007180

[…] go terms in the pairwise stage comparisons., htsfilter [] was used with default parameters to discard lowly expressed genes across all samples. the function poismixcluswrapper from the library htscluster [] was applied on the rest of genes with the parameters: gmin = 1, gmax = 25, lib.type =“deseq”., different model selection approaches are used by htscluster (i.e. to identify the number […]

PMCID: 5445279
PMID: 28545577
DOI: 10.1186/s12870-017-1037-z

[…] 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 []. […]

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

[…] 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 […]

PMCID: 5085048
PMID: 27792774
DOI: 10.1371/journal.pntd.0005067

[…] analyses between samples of t. brasiliensis, taking into account their environment (sylvatic, peridomiciliary and domiciliary) and sex. we also searched clusters of co-expressed contigs using htscluster. among differentially expressed (de) contigs, most were under-expressed in the chemosensory organs of the domiciliary bugs compared to the other samples and in females compared to males. […]

PMCID: 4256448
PMID: 25473826
DOI: 10.1371/journal.pone.0114598

[…] we adopted the term of “co-abundance” when referring to plasma mirnas. groups of co-abundant mirnas were identified from the mirna-seq data using the clustering approach implemented in the r package htscluster (version 1.2) . briefly, we assumed that the population of mirnas arises from several distinct subpopulations or clusters, each of which can be modeled separately. the filtered population […]


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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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