MmPalateMiRNA-package: R package compendium for the analysis of murine palate...
In MmPalateMiRNA: Murine Palate miRNA Expression Analysis
Description
Details
Author(s)
References
Description
R package compendium for the analysis of two-color miRNA expression
data, during the period of murine embryonic palate development
(gestational days (GD) 12, 13, and 14). Samples were hybridized to
Miltenyi Biotech miRXplore Microarrays.
The compendium covers a wide range of
steps which occur in a typical miRNA microarray data analysis, including
pre-processing, normalization, differential expression analysis,
clustering, target identification, and gene-set enrichment analysis.
Details
Package: MmPalateMiRNA
Type: Package
Version: 1.0
Date: 2011-09-14
License: LGPL
LazyLoad: yes
The package contains several functions which are helpful during the
pre-processing steps of array data, which are specific to
RGList objects and, in the case of the
fixOutliers and fixMVs functions, depend on
the replicated structure of Miltenyi Biotech miRXplore
Microarrays. Additionally, methods are available to produce diagnostic plots
for RGList objects and lists of
normalized data sets (MAList and /
or NChannelSet objects), which
build on the generic functions in lattice.
Lastly, the main focus of the package is the package
vignette "MmPalateMiRNA", which contains an extended example covering
the typical steps in an miRNA microarray data analysis.
Author(s)
Guy Brock, Partha Mukhopadhyay, Vasyl Pihur, Bob Green, M. Michele Pisano
Maintainer: Guy Brock <guy.brock@louisville.edu>
References
P. Mukhopadhyay, G. Brock, V. Pihur, C. Webb, M.M. Pisano, and R.M. Greene.
Developmental microRNA expression profiling of murine embryonic orofacial tissue.
Birth Defects Res A Clin Mol Teratol, 88(7):511-34, 2010.
R. Gentleman.
Reproducible research: a bioinformatics case study.
Stat Appl Genet Mol Biol, 4:Article2, 2005.
D. Sarkar, R. Parkin, S. Wyman, A. Bendoraite, C. Sather, J. Delrow, A. K. Godwin,
C. Drescher, W. Huber, R. Gentleman, and M. Tewari.
Quality assessment and data analysis for microRNA expression arrays.
Nucleic Acids Res, 37(2):e17, 2009.
MmPalateMiRNA documentation built on April 28, 2020, 7:54 p.m.
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Description Details Author(s) References
Description
R package compendium for the analysis of two-color miRNA expression data, during the period of murine embryonic palate development (gestational days (GD) 12, 13, and 14). Samples were hybridized to Miltenyi Biotech miRXplore Microarrays. The compendium covers a wide range of steps which occur in a typical miRNA microarray data analysis, including pre-processing, normalization, differential expression analysis, clustering, target identification, and gene-set enrichment analysis.
Details
| Package: | MmPalateMiRNA |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2011-09-14 |
| License: | LGPL |
| LazyLoad: | yes |
The package contains several functions which are helpful during the
pre-processing steps of array data, which are specific to
RGList objects and, in the case of the
fixOutliers and fixMVs functions, depend on
the replicated structure of Miltenyi Biotech miRXplore
Microarrays. Additionally, methods are available to produce diagnostic plots
for RGList objects and lists of
normalized data sets (MAList and /
or NChannelSet objects), which
build on the generic functions in lattice.
Lastly, the main focus of the package is the package
vignette "MmPalateMiRNA", which contains an extended example covering
the typical steps in an miRNA microarray data analysis.
Author(s)
Guy Brock, Partha Mukhopadhyay, Vasyl Pihur, Bob Green, M. Michele Pisano Maintainer: Guy Brock <guy.brock@louisville.edu>
References
P. Mukhopadhyay, G. Brock, V. Pihur, C. Webb, M.M. Pisano, and R.M. Greene. Developmental microRNA expression profiling of murine embryonic orofacial tissue. Birth Defects Res A Clin Mol Teratol, 88(7):511-34, 2010.
R. Gentleman. Reproducible research: a bioinformatics case study. Stat Appl Genet Mol Biol, 4:Article2, 2005.
D. Sarkar, R. Parkin, S. Wyman, A. Bendoraite, C. Sather, J. Delrow, A. K. Godwin, C. Drescher, W. Huber, R. Gentleman, and M. Tewari. Quality assessment and data analysis for microRNA expression arrays. Nucleic Acids Res, 37(2):e17, 2009.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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