oposSOM: Comprehensive analysis of transciptome data

This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("oposSOM")
AuthorHenry Loeffler-Wirth <wirth@izbi.uni-leipzig.de> and Martin Kalcher <mkalcher@porkbox.net>
Bioconductor views DataRepresentation DifferentialExpression GeneExpression GeneSetEnrichment Visualization
Date of publicationNone
MaintainerHenry Loeffler-Wirth <wirth@izbi.uni-leipzig.de>
LicenseGPL (>=2)
Version1.14.0
http://som.izbi.uni-leipzig.de

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/affymetrix_quality_check.r R/biomart_available.r R/calc_statistics.r R/cancer_hallmarks.r R/check_input_parameters.r R/chromosome_expression_reports.r R/detect_ensembl_dataset.r R/detect_spots_integral.r R/detect_spots_samples.r R/difference_analyses.r R/entropy_profiles.r R/gene_lists.r R/geneset_analysis.r R/geneset_overviews.r R/geneset_profiles_and_maps.r R/geneset_statistic_integral.r R/geneset_statistic_samples.r R/get_running_average.r R/get_statistic.r R/group_analyses.r R/group_assignment.r R/group_specific_genesets.r R/heatmaps.r R/html_differences_summary.r R/html_geneset_analysis.r R/html_group_summary.r R/html_module_summary.r R/html_sample_summary.r R/html_summary.r R/module_correlation_map.r R/modules_CSV.r R/modules_chromosomes.r R/modules_profiles.r R/modules_relations.r R/modules_reports.r R/opossom.r R/pat_assignment.r R/prepare_annotation.r R/primary_analysis.r R/quality_check.r R/quantile_normalization.r R/radarchart.r R/sample_expression_portraits.r R/sample_similarity_analysis_ED.r R/sample_similarity_analysis_ICA.r R/sample_similarity_analysis_SOM.r R/sample_similarity_analysis_cor.r R/summary_sheets_groups.r R/summary_sheets_modules.r R/summary_sheets_pats.r R/summary_sheets_samples.r R/supporting_maps.r R/topology_profiles.r R/util.r
build
build/vignette.rds
data
data/datalist
data/opossom.genesets.RData
data/opossom.tissues.RData
inst
inst/CITATION
inst/doc
inst/doc/Vignette.R
inst/doc/Vignette.Rnw
inst/doc/Vignette.pdf
man
man/oposSOM-package.Rd man/opossom.genesets.Rd man/opossom.new.Rd man/opossom.run.Rd man/opossom.tissues.Rd
vignettes
vignettes/HTML.pdf
vignettes/SizeRecommendation.pdf
vignettes/Summary.pdf
vignettes/Vignette.Rnw
vignettes/opossom.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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