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coseq specifications

Information


Unique identifier OMICS_13307
Name coseq
Alternative name Co-Expression Analysis of Sequencing Data
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data RNA sequence
Output data Parameter estimation, model selection
Operating system Unix/Linux
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.99.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Andrea Rau

Publication for Co-Expression Analysis of Sequencing Data

coseq citations

 (2)
library_books

Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle

2018
BMC Genomics
PMCID: 5936029
PMID: 29728057
DOI: 10.1186/s12864-018-4668-z

[…] laying, post-lay, emerg) by calculating a likelihood ratio test of the full model (~stage) against the reduced model (~ 1), and retaining contigs with a bh-adjusted p-value < 0.10. using the coseq bioconductor package version 0.99.12 [], a gaussian mixture model was fit to the arcsine-transformed normalized profiles of differentially expressed contigs for k = 2, …, 50 clusters. based […]

library_books

Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments

2005
Nucleic Acids Res
PMCID: 1087784
PMID: 15860776
DOI: 10.1093/nar/gki535

[…] 800 16s rrna sequences and 805 23s rrna sequences were aligned; for eukarya (e), 5190 18s rrna sequences and 133 28s rrna sequences were considered (). the sequence alignments were analyzed using coseq, bioedit () and rnamlview to determine covariations and substitutions at sequence positions corresponding to non-wc pairs observed in crystal structures and to compare […]


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coseq institution(s)
GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France; Institut de Mathématiques de Toulouse, INSA de Toulouse, Université de Toulouse, Toulouse, France
coseq funding source(s)
The authors acknowledge the support of the French Agence Nationale de la Recherche (ANR), under grant MixStatSeq (ANR-13-JS01-0001-01).

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