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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

Versioning


No version available

Documentation


Maintainer


  • person_outline Andrea Rau

Publication for HTSCluster

HTSCluster citations

 (6)
library_books

Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood brain barrier integrity

2018
PLoS Genet
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 […]

library_books

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

[…] 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 []. […]

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

[…] 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 […]

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

[…] 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. […]

library_books

Impact of the Genetic Background on the Composition of the Chicken Plasma MiRNome in Response to a Stress

2014
PLoS One
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 […]

library_books

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

[…] 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 […]


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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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