| affy.pivot.table | merge expression and calls together |
| average.replicates.gct | Average replicate columns from within a gct file Average... |
| catplot.GSEA | Function to generate CAT plots for >= 2 GSEA comparisons |
| catplot.GSEA.2way | Plot a CAT plot upon 2 GSEA objects. |
| catplot.GSEA.2way.vs.random | Compare 2 GSEA runs via CAT plots & estimate the expected... |
| catplot.GSEA.random | Compare multiple GSEA runs via CAT plots & estimate the... |
| chip2description | Convert a GSEA chip file or object into a vector of... |
| collapse.gct | Collapse a GCT object |
| collapse.gct2geneset | Collapse a GCT file from 1 row per gene to 1 row per geneset. |
| collapse.gct.file | Collapse a GCT file |
| convert.gct2submap | Prepare data for use in SubMap. |
| convert.gsea.res2gct | Convert a res object to a gct object. |
| dist.gsea | Determine the distance between various leading edge genes, in... |
| export.broad.cls | Export a cls file for GenePattern. Export a cls file for... |
| export.broad.res | Export a res file for GenePattern. |
| export.gsea | Export a gsea object to the filesystem. |
| export.gsea.cdt | Cluster leading edge genesets, and export in Stanford cdt/gtr... |
| export.gsea.chip | Export a GSEA chip file Export a GSEA chip file - this... |
| export.gsea.edb | Export a GSEA edb object to an 'XML' file. |
| export.gsea.gct | Function to export a GenePattern gct file. |
| export.gsea.gct.topTable | Export a GCT file, from a GSEA topTable plus data table |
| export.gsea.gmt | Export a gmt file Genesets for BROAD's GSEA are usually... |
| export.gsea.gtr | You should use export.gsea.cdt instead. |
| export.gsea.leadingedge.analysis | Export the plots and tables required for a GSEA leading edge... |
| export.gsea.odf | Export a table of data to a GenePattern odf file |
| export.gsea.odf.lmFit | Export a limma lmFit to a GSEA ODF file. From two linear... |
| export.gsea.rnk | Export a vector of values as a GSEA pre-ranked list. |
| export.gsea.rnk.topTable | Export a limma topTable to a GSEA pre-ranked list. The 'rnk'... |
| export.gsea.rpt | Export a GSEA rpt file |
| genepattern2spd | GenePattern to SPD |
| genepattern.HeatMapImage | From a GCT file, create a HeatMap Image, using the jar from... |
| GMThyperGTest | Perform a Hypergeometric test, upon a GMT file. Much like... |
| gsea2adjmat | Convert a GSEA object into an adjacency matrix at the... |
| gsea.combine | Combine N gsea runs together |
| gsea.compare.runs.1gmt | Compare N GSEA runs vs a single gmt file (eg lots of rnk... |
| gsea.compare.runs.filter | Function to filter a set of GSEA run comparisons, and/or to... |
| gsea.compare.runs.sort | Function to sort the rows of a GSEA comparison object |
| gsea.convert.clm2cls | Convert a clm file into a cls file. |
| gsea.filter | Take a GSEA list, and filter out genesets that fail various... |
| gsea.filter.edb | Filter a GSEA edb file, restricting the entries to restricted... |
| gsea.fix.output | Fix the output from a GSEA run |
| gsea.fix.output.detailed.enrichment.results.html | fix the "Detailed enrichment results in html format" 2 pages. |
| gsea.fix.output.geneset.report | fix an individual GSEA GeneSet html report. |
| gsea.fix.output.index.html | fix the index.html file |
| gsea.gct.probes2genes | Convert probe-level to gene-level gct |
| gsea.gct.select.features.columns | Restrict the number of columns in a gct & cls file. |
| gsea.gct.select.features.rows | Subset the rows of a gct file. The GenePattern... |
| gsea.genesets2gct | Create gct files for all gseaPreranked runs comparing 1 rnk... |
| gsea.hardwire.rpt.paths | Rewire the file locations referenced within a GSEA rpt file. |
| GSEAhyperGTest | Perform a Hypergeometric test, upon a GMT file. This is a... |
| gsea.leadingedge.distance | Determine the distance between various leading edge genes, in... |
| gsea.length | How many genesets in a GSEA object? |
| gsealist2adjmat | Convert a GSEA list into an adjacency matrix at the... |
| gsealist2genesetlist | Extract the geneset names from a list of GSEA objects. |
| gsealist.find.geneset | From a list of GSEA's, find the elements that contain... |
| gsea.merge | Merge two GSEA objects. |
| gsea.merge.dirs | Merge 2 gsea runs, by referencing only the GSEA directories. |
| gsea.merge.edb | Merge two GSEA edb objects. |
| gsea.merge.edb.dirs | Function to merge the edb files from 2 GSEA runs. |
| gsea.merge.tt | Merge N GSEA toptables, retaining a column of interest (eg... |
| gsea.rename.genesets | Rename the genesets from within a GSEA object. |
| gsea.rename.genesets.edb | Parse an edb XML object, and rename the genesets with... |
| gsea.reorder.gmt.by.rnk | Reorder the genes within a gmt object to match the order of... |
| gsea.split | Split a GSEA object based on leading edge similarities. Take... |
| gsea.summarise | Summarise GSEA results |
| gsea.topTable.sort | sort a GSEA topTable |
| gsea.which.gmt | What gmt file was used? |
| import.genepattern.odf | import.genepattern.odf |
| import.gsea | Import the results from a GSEA or GseaPreRanked analysis. |
| import.gsea.chip | Import a GSEA chip file. This can look inside a gsea output... |
| import.gsea.clm | Import a clm file |
| import.gsea.cls | Import a cls file |
| import.gsea.compare.runs | Import the output produced by gsea.compare.runs.sh |
| import.gsea.edb | Import a GSEA edb file. The edb file is a machine readable... |
| import.gsea.gct | Import a gct file |
| import.gsea.gmt | Import a gmt file that is commonly used by Broad's GSEA. |
| import.gsea.gmx | Import a gmx file that is commonly used by Broad's GSEA. |
| import.gsea.leadingedge | Import the leading edge subset of genes from each category.... |
| import.gsea.res | Import a GenePattern res file |
| import.gsea.rnk | Import a rnk file used for running GSEA PreRanked. |
| import.gsea.rpt | Import the rpt file from a GSEA, or GseaPreRanked analysis... |
| import.gsea.topTable | Import the tabular results from a GSEA PreRanked run |
| is.gsea | Is x a GSEA object |
| is.gsea.dir | is the argument a valid GSEA directory? |
| is.gsea.gct.file | is.gsea.gct.file |
| is.gsea.list | is 'x' a gsea list, that is, a list containing gsea results? |
| is.gsea.res.file | is.gsea.res.file |
| is.gsea.zip | Is the argument a GSEA zip file? |
| jacquard-methods | The Jacquard coefficient as a measure of overlap in terms of... |
| metaGSEA-package | Meta-analysis of GSEA analyses, including intra- and... |
| plclust.gsea | Plot an hclust object, that has been made from GSEA genesets. |
| plclust_in_colour | modifiction of plclust for plotting hclust objects *in... |
| plot_gseacmp.barplot | Taking a gseacmp object (see gsea.compare.runs.1gmt), create... |
| plot_gsea.leadingedge | Combination GSEA Leading Edge plot. |
| plot_gsea.leadingedge.adjmat | Generate a binary adjacency matrix image (like a heatmap with... |
| plot_gsea.leadingedge.barplot | GSEA Leading Edge analysis: Barplot of number of genesets... |
| plot_gsea.leadingedge.barplot.auto | Function to automatically plot barplot's of filtered GSEA... |
| plot_gsea.leadingedge.HCL | GSEA Leading Edge HCL plot. |
| plot_gsea.leadingedge.HCL.1clusterPerPage | Take a GSEA object, do an HCL between the leading edge genes,... |
| plot_gsea.leadingedge.HCL.auto | Automated GSEA HCL |
| plot_gsea.leadingedge.HCL.simple | Take a GSEA object and calculate an HCL between the leading... |
| plot_gsea.leadingedge.heatmap | Generate a heatmap of genesets from a GSEA run |
| plot_gsea.leadingedge.heatmap.auto | Generate a heatmap of genesets from a GSEA run, across a... |
| plot_gsea.res | Boxplot the intensities for an array split by the detection... |
| plot_gsea.statistic.histograms | plot a panel of gsea histograms From a GSEA object, plot a... |
| plot_gsea.venn | Compare the significant genesets from 2 or 3 GSEA runs using... |
| plot_gsea.venn.auto | Plot a Venn diagram of overlaps between genesets from >= 2... |
| print.gsea.venn | Print a Venn diagram of overlaps between genesets from >= 2... |
| qplot.data | .qplot.data This code is taken from qvalue::qplot (from... |
| reorder.gct | Function to reorder the rows of a GCT object |
| reorder.gct.file | Reorder the rows of a GCT file. |
| subset.gsea | Subsetting GSEA objects. Return subsets of GSEA objects which... |
| test.broad.ftp | test whether a connection to BROAD's FTP/HTTP sites can be... |
