ExomeDepth protocols

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description
ExomeDepth computational protocol

ExomeDepth specifications

Information


Unique identifier OMICS_05443
Name ExomeDepth
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 1.1.10
Stability Stable
Requirements
methods, IRanges, Rsamtools, Biostrings, GenomicAlignments, knitr, R(≥3.3.0), GenomicRanges(≥1.23.0), aod, VGAM(≥0.8.4)
Source code URL https://cran.r-project.org/src/contrib/ExomeDepth_1.1.10.tar.gz
Maintained Yes

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Documentation


Maintainer


  • person_outline Vincent Plagnol <>

Publication for ExomeDepth

ExomeDepth IN pipelines

 (2)
2017
PMCID: 5886296
PMID: 29228333
DOI: 10.1093/hmg/ddx422

[…] the charity open access fund (coaf) to the university of leeds., babraham bioinformatics: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, cut adapt: https://github.com/marcelm/cutadapt, exomedepth: https://cran.r-project.org/web/packages/exomedepth/, picard: http://broadinstitute.github.io/picard/, vcfhacks: https://github.com/gantzgraf/vcfhacks; all web-sites date last accessed […]

2017
PMCID: 5886296
PMID: 29228333
DOI: 10.1093/hmg/ddx422

[…] of leeds., babraham bioinformatics: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, cut adapt: https://github.com/marcelm/cutadapt, exomedepth: https://cran.r-project.org/web/packages/exomedepth/, picard: http://broadinstitute.github.io/picard/, vcfhacks: https://github.com/gantzgraf/vcfhacks; all web-sites date last accessed october […]

ExomeDepth institution(s)
UCL Genetics Institute, UCL, London, UK; Department of Medicine, University of Cambridge, Cambridge, UK; UCL CoMPLEX program, London, UK; UCL Institute of Neurology, UCL, London, UK; Royal London Hospital, London, UK; Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK; Molecular Immunology Unit, Wolfson Centre for Gene Therapy of Childhood Disease, UCL Institute of Child Health, Great Ormond Street Hospital for Children, London, UK; Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital, Cambridge, UK
ExomeDepth funding source(s)
Supported by a Wellcome Trust Senior Research Fellow in Basic Biomedical Science (095198/Z/10/Z); the Wellcome Trust grant (088838/Z/09/Z), the Royal Society Research grant RG090638, the EU FP7 grant (261441) (PEVNET project) and the ERC Starting grant (260477); the NIHR Cambridge Biomedical Research Centre; MRC research grant (G1001158) and the NIHR Moorfields Biomedical Research Council grant.

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