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.

Author
Henry Loeffler-Wirth <wirth@izbi.uni-leipzig.de> and Martin Kalcher <mkalcher@porkbox.net>
Date of publication
None
Maintainer
Henry Loeffler-Wirth <wirth@izbi.uni-leipzig.de>
License
GPL (>=2)
Version
1.12.0
URLs

View on Bioconductor

Man pages

opossom.genesets
Additional literature genesets
opossom.new
Initialize the oposSOM pipeline.
oposSOM-package
Comprehensive analysis of transciptome data
opossom.run
Execute the oposSOM pipeline.
opossom.tissues
Example data set.

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