REDseq specifications

Information


Unique identifier OMICS_16069
Name REDseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data The output directory contains the shortest paths from a source protein to the target proteins.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.26.0
Stability Stable
Requirements
AnnotationDbi, stats, graphics, BiocGenerics, utils, R(>=2.15.0), Biostrings, BSgenome, ChIPpeakAnno, multtest, BiocGenerics(>=0.1.0), BSgenome.Celegans.UCSC.ce2, IRanges(>=1.13.5)
Maintained Yes

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Documentation


Maintainer


  • person_outline Lihua Julie Zhu <>

REDseq in publications

 (3)
PMCID: 4604252
PMID: 25937343
DOI: 10.1016/j.mcn.2015.04.007

[…] and assembled into figures with quarkxpress (pantone)., ensembl genome browser, http://www.ensembl.org/index.html, ucsc genome browser, http://genome.ucsc.edu, refseq, http://www.ncbi.nlm.nih.gov/redseq, mouse genome informatix, http://www.informatics.jax.org/, on-line mendelian inheritance in man (omim), http://www.omim.org/, ts-coexp browser, http://www.mbcunito.it/cbu/ts-coexp., to verify […]

PMCID: 4558864
PMID: 26245677
DOI: 10.1093/gbe/evv147

[…] from treebase (http://treebase.org/treebase-web/search/study/summary.html?id=15150&x-access-code=7bdd870b7e5e820b3737098d36e3cec4&agreement=ok), the redtol website (dbdata.rutgers.edu/redseq/), and from the corresponding author upon request., the phylogeny and statistical support for monophyletic groups were inferred using the maximum-likelihood (ml and ml bootstrap analysis) […]

PMCID: 4378318
PMID: 25494698
DOI: 10.1186/1471-2164-15-1104

[…] of the expected product of sau96i digestion (gncc) immediately following the adapter barcode confirmed the quality of the libraries (figure┬ác).figure 1, we developed a software package (also named redseq; available as a bioconductor package) to assign each read to a unique rs in the mouse genome (see methods for details), and count the relative cut frequency per site corresponding […]


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