clusterSeq statistics

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clusterSeq specifications

Information


Unique identifier OMICS_20498
Name clusterSeq
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 3.0
Computer skills Advanced
Version 1.4.0
Stability Stable
Requirements
methods, stats, graphics, BiocGenerics, utils, BiocStyle, BiocParallel, R(>=3.0.0), baySeq
Maintained Yes

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Maintainer


  • person_outline Thomas J. Hardcastle <>

Publication for clusterSeq

clusterSeq in pipeline

2018
PMCID: 5878008
PMID: 29440499
DOI: 10.1073/pnas.1718263115

[…] expressed genes for each library (). analyses of the data were carried out using the r package bayseq (), and clustering based on the posterior probabilities was acquired from this package and the clusterseq package (). the go enrichment analysis on grafting-specific genes was done with a customized r script (https://github.com/alexga/graftingscripts) using the package gostats ()., we thank […]


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clusterSeq in publications

 (2)
PMCID: 5878008
PMID: 29440499
DOI: 10.1073/pnas.1718263115

[…] expressed genes for each library (). analyses of the data were carried out using the r package bayseq (), and clustering based on the posterior probabilities was acquired from this package and the clusterseq package (). the go enrichment analysis on grafting-specific genes was done with a customized r script (https://github.com/alexga/graftingscripts) using the package gostats ()., we thank […]

PMCID: 5825147
PMID: 29432417
DOI: 10.1371/journal.pcbi.1005954

[…] randomly and passed to the next generation (). as a first step, we confirmed the porter simulation results using the code that was published with porter’s paper [] (https://github.com/adaptivegenome/clusterseq/). we ran simulations starting with c = 14,000 clones uniformly distributed over 3 ⋅ 105 cells and r=2419log(2) to match the experimentally observed doubling time of 19 hours. as expected, […]


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clusterSeq institution(s)
Department of Plant Sciences, University of Cambridge, Cambridge, UK; European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
clusterSeq funding source(s)
Supported by European Research Council Advanced Investigator Grant ERC-2013-AdG 340642.

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