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.

AuthorHenry Loeffler-Wirth <wirth@izbi.uni-leipzig.de> and Martin Kalcher <mkalcher@porkbox.net>
Date of publicationNone
MaintainerHenry Loeffler-Wirth <wirth@izbi.uni-leipzig.de>
LicenseGPL (>=2)
Version1.12.0
http://som.izbi.uni-leipzig.de

View on Bioconductor

Files in this package

oposSOM/DESCRIPTION
oposSOM/NAMESPACE
oposSOM/NEWS
oposSOM/R
oposSOM/R/2nd_lvl_component_analysis.r
oposSOM/R/2nd_lvl_correlation_analysis.r
oposSOM/R/2nd_lvl_module_correlation_map.r
oposSOM/R/2nd_lvl_similarity_analysis.r
oposSOM/R/2nd_lvl_som.r
oposSOM/R/3rd_lvl_chromosomal_enrichment.r
oposSOM/R/3rd_lvl_networks.r
oposSOM/R/3rd_lvl_summary_sheets.r
oposSOM/R/affymetrix_quality_check.r
oposSOM/R/biomart_available.r
oposSOM/R/calc_statistics.r
oposSOM/R/cancer_hallmarks.r
oposSOM/R/chromosome_expression_reports.r
oposSOM/R/detect_ensembl_dataset.r
oposSOM/R/detect_spots_integral.r
oposSOM/R/detect_spots_samples.r
oposSOM/R/difference_analyses.r
oposSOM/R/entropy_profiles.r
oposSOM/R/gene_lists.r
oposSOM/R/geneset_analysis.r
oposSOM/R/geneset_overviews.r
oposSOM/R/geneset_profiles_and_maps.r
oposSOM/R/geneset_statistic_integral.r
oposSOM/R/geneset_statistic_samples.r
oposSOM/R/get_running_average.r
oposSOM/R/get_statistic.r
oposSOM/R/group_analyses.r
oposSOM/R/group_assignment.r
oposSOM/R/group_specific_genesets.r
oposSOM/R/heatmaps.r
oposSOM/R/html_differences_summary.r
oposSOM/R/html_geneset_analysis.r
oposSOM/R/html_group_summary.r
oposSOM/R/html_integral_summary.r
oposSOM/R/html_sample_summary.r
oposSOM/R/html_summary.r
oposSOM/R/opossom.r
oposSOM/R/pat_assignment.r
oposSOM/R/prepare.r
oposSOM/R/prepare_annotation.r
oposSOM/R/quality_check.r
oposSOM/R/quantile_normalization.r
oposSOM/R/radarchart.r
oposSOM/R/sample_expression_portraits.r
oposSOM/R/sample_rank_maps.r
oposSOM/R/smooth_scatterplot.r
oposSOM/R/summary_sheets_groups.r
oposSOM/R/summary_sheets_integral.r
oposSOM/R/summary_sheets_pats.r
oposSOM/R/summary_sheets_samples.r
oposSOM/R/supporting_maps.r
oposSOM/R/topology_profiles.r
oposSOM/R/util.r
oposSOM/build
oposSOM/build/vignette.rds
oposSOM/data
oposSOM/data/datalist
oposSOM/data/opossom.genesets.RData
oposSOM/data/opossom.tissues.RData
oposSOM/inst
oposSOM/inst/CITATION
oposSOM/inst/doc
oposSOM/inst/doc/Vignette.R
oposSOM/inst/doc/Vignette.Rnw
oposSOM/inst/doc/Vignette.pdf
oposSOM/man
oposSOM/man/oposSOM-package.Rd oposSOM/man/opossom.genesets.Rd oposSOM/man/opossom.new.Rd oposSOM/man/opossom.run.Rd oposSOM/man/opossom.tissues.Rd
oposSOM/vignettes
oposSOM/vignettes/HTML.pdf
oposSOM/vignettes/SizeRecommendation.pdf
oposSOM/vignettes/Summary.pdf
oposSOM/vignettes/Vignette.Rnw
oposSOM/vignettes/opossom.bib

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