GenePattern module repository: All modules

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ModuleType
ARACNE
Runs the ARACNE algorithm for reverse engineering cellular networks
Version: 2 		Pathway Analysis
 
AreaChange
Calculates fraction of area under the spectrum that is attributable to signal (area after noise removal / original area)
Version: 2 		Proteomics
 
CART
Classification and Regression Tree
Version: 2 		Prediction
 
CARTXValidation
Classification and Regression Tree X-Validation
Version: 2 		Prediction
 
ClassNeighbors
Select genes that most closely resemble a profile
Version: 1 		Gene List Selection
 
ComparativeMarkerSelection
Computes significance values for features using several metrics, including FDR(BH), Q-Value, maxT, FWER, Feature-Specific P-Value, and Bonferroni.
Version: 4 		Gene List Selection
 
ComparativeMarkerSelectionViewer
Views the results from ComparativeMarkerSelection
Version: 4 		Visualizer
 
CompareSpectra
Compares two spectra to determine similarity
Version: 2 		Proteomics
 
ConsensusClustering
Resampling-based clustering method
Version: 5 		Clustering
 
ConvertLineEndings
Converts line endings to the host operating system's format.
Version: 1 		Preprocess & Utilities
 
ConvertToMAGEML
Converts a gct, res, or odf dataset file to a MAGE-ML file
Version: 1 		Preprocess & Utilities
 
CopyNumberDivideByNormals
Determines the copy number of a target SNP
Version: 2 		SNP Analysis
 
CytoscapeViewer
Visualizes a gene network
Version: 2 		Visualizer
 
DownloadURL
Downloads a file from a URL
Version: 1 		Preprocess & Utilities
 
ExpressionFileCreator
Creates a RES or GCT file from a set of Affymetrix CEL files
Version: 6 		Preprocess & Utilities
 
ExtractColumnNames
Lists the sample descriptors from a .res file.
Version: 2 		Preprocess & Utilities
 
ExtractComparativeMarkerResults
Creates a derived dataset and feature list file from the results of ComparativeMarkerSelection
Version: 3 		Gene List Selection
 
ExtractRowNames
Extracts the row names from a .res, .gct, or .odf file.
Version: 3 		Preprocess & Utilities
 
FeatureSummaryViewer
Feature Summary Viewer
Version: 3 		Visualizer
 
GEOImporter
Imports data from the Gene Expression Omnibus (GEO)
Version: 5 		Preprocess & Utilities
 
GISTIC
Genomic Identification of Significant Targets in Cancer
Version: 1 		SNP Analysis
 
GLAD
Gain and Loss Analysis of DNA
Version: 2 		SNP Analysis
 
GSEA
Gene Set Enrichment Analysis
Version: 1 		Gene List Selection
 
GSEALeadingEdgeViewer
Leading Edge Viewer for GSEA results
Version: 1 		Visualizer
 
GeneCruiser
Retrieve gene annotations for Affy probe ids from GeneCruiser
Version: 5 		Annotation
 
GeneListSignificanceViewer
Views the results of marker analysis
Version: 4 		Visualizer
 
GeneNeighbors
Select genes that most closely resemble a continuous profile (e.g., another gene)
Version: 2 		Gene List Selection
 
GlobalAlignment
standard global sequence analysis
Version: 0 		Sequence Analysis
 
Golub.Slonim.1999.Science.all.aml.pipeline
ALL/AML methodology, from Golub and Slonim et al., 1999
Version: 1 		pipeline
 
HeatMapImage
Creates a heat map from a dataset
Version: 6 		Image Creators
 
HeatMapViewer
Displays a heat map
Version: 8 		Visualizer
 
HierarchicalClustering
Hierarchical Clustering
Version: 3 		Clustering
 
HierarchicalClustering.MATLAB
Hierarchical Clustering
Version: 0 		Clustering
 
HierarchicalClusteringImage
Creates an image of the dendrogram generated from HierarchicalClustering
Version: 2 		Image Creators
 
HierarchicalClusteringImage.MATLAB
Hierarchical Clustering Image
Version: 0 		Image Creators
 
HierarchicalClusteringViewer
Views results of hierarchical clustering.
Version: 8 		Visualizer
 
Hu68kHu35kAtoU95
Converts a list of Affymetrix Hu6800/Hu35KsubA probes to the corresponding Affymetrix U95Av2 probes.
Version: 1 		Preprocess & Utilities
 
ImputeMissingValues.KNN
Imputes missing values (Windows only)
Version: 9 		Missing Value Imputation
 
JavaTreeView
Hierarchical clustering viewer that reads in Eisen's cdt, atr, and gtr files. A detailed description of these formats is available from http://microarray.ccgb.umn.edu/smd/html/MicroArray/help/formats.shtml
Version: 2 		Visualizer
 
KMeansClustering
Module that performs the K-Means Clustering algorithm
Version: 1 		Clustering
 
KNN
K-nearest neighbors classification
Version: 3 		Prediction
 
KNNXValidation
KNN classification with Leave-One-Out Cross-Validation
Version: 5 		Prediction
 
KSscore
Computes the Kolmogorov-Smirnov score for a set of genes within an ordered list.
Version: 1 		Statistical Methods
 
LOHPaired
Computes LOH for paired samples
Version: 3 		SNP Analysis
 
LandmarkMatch
A proteomics method to propogate identifed peptides across multiple MS runs
Version: 2 		Proteomics
 
LocatePeaks
Locates detected peaks in a spectrum.
Version: 2 		Proteomics
 
Lu.Getz.Miska.Nature.June.2005.PDT.mRNA.pipeline
PNN Prediction using mRNA
Version: 0 		pipeline
 
Lu.Getz.Miska.Nature.June.2005.PDT.miRNA.pipeline
PNN Prediction using mRNA
Version: 0 		pipeline
 
Lu.Getz.Miska.Nature.June.2005.clustering.ALL.pipeline
Hierarchical clustering of 73 ALL samples with various types of genetic alterations
Version: 0 		pipeline
 
Lu.Getz.Miska.Nature.June.2005.clustering.ep.mRNA.pipeline
Hierarchical clustering of 89 epithelial samples in mRNA space
Version: 0 		pipeline
 
Lu.Getz.Miska.Nature.June.2005.clustering.ep.miRNA.pipeline
Hierarchical clustering of 89 epithelial samples in miRNA space.
Version: 0 		pipeline
 
Lu.Getz.Miska.Nature.June.2005.clustering.miGCM218.pipeline
Hierarchical clustering of 218 samples from various tissue types as published in Lu, Getz, Miska et al., Nature, 9 June 2005
Version: 0 		pipeline
 
Lu.Getz.Miska.Nature.June.2005.mouse.lung.pipeline
Normal/tumor classifier and kNN prediction of mouse lung samples
Version: 1 		pipeline
 
MAGEMLImportViewer
A visualizer to import data in MAGE-ML format into GenePattern
Version: 2 		Visualizer
 
MINDY
Runs the MINDY algorithm for inferring genes that modulate the activity of a transcription factor at post-transcriptional levels
Version: 1 		Pathway Analysis
 
MINDYViewer
Visualizes the results of MINDY
Version: 1 		Visualizer
 
MapChipFeaturesGeneral
Change (map) the features (genes) of a dataset
Version: 1 		Preprocess & Utilities
 
MergeColumns
Merge datasets by column.
Version: 1 		Preprocess & Utilities
 
MergeRows
Merge datasets by row.
Version: 1 		Preprocess & Utilities
 
Multiplot
Creates customizable plots of expression data-derived data.
Version: 1 		Visualizer
 
MultiplotExtractor
Creates customizable plots of expression data-derived data.
Version: 1 		Visualizer
 
MultiplotPreprocess
Creates derived data from an expression dataset for use in the Multiplot Visualizer module
Version: 1 		Preprocess & Utilities
 
NMF
Non-negative Matrix Factorization
Version: 2 		Projection
 
NMFConsensus
Non-negative Matrix Factorization (NMF) Consensus Clustering
Version: 4 		Clustering
 
PCA
Principal Component Analysis (adapted from MeV, http://www.tigr.org/software/tm4/mev.html)
Version: 3 		Projection
 
PCAViewer
Principal Component Analysis Visualizer (adapted from MeV, http://www.tigr.org/software/tm4/mev.html)
Version: 4 		Visualizer
 
PNN
Probabilistic Neural Network (PNN)
Version: 0 		Prediction
 
PNNXValidationOptimization
PNN Leave-One-Out Cross-Validation Optimization
Version: 0 		Prediction
 
PeakMatch
Perform peak matching on LC-MS data
Version: 2 		Proteomics
 
Peaks
Determine peaks in the spectrum using a series of digital filters.
Version: 2 		Proteomics
 
PlotPeaks
Plot peaks
Version: 2 		Proteomics
 
PredictionResultsViewer
Visualizes prediction results
Version: 4 		Visualizer
 
PreprocessDataset
Performs several preprocessing options on a res, gct, or Dataset input file
Version: 3 		Preprocess & Utilities
 
ProteoArray
LC-MS proteomic data processing module
Version: 1 		Proteomics
 
ProteomicsAnalysis
Runs the proteomics analysis on the set of input spectra
Version: 2 		Proteomics
 
ReorderByClass
Reorder the samples in an expression dataset and class file by class
Version: 2 		Preprocess & Utilities
 
SNPFileCreator
Process Affymetrix SNP probe-level data into an expression value
Version: 1 		SNP Analysis
 
SNPFileSorter
Sorts a .snp file by Chromosome and location
Version: 1 		SNP Analysis
 
SNPMultipleSampleAnalysis
Determine Regions of Concordant Copy Number Aberrations
Version: 1 		SNP Analysis
 
SOMClusterViewer
Visualize clusters created with the SOM algorithm
Version: 5 		Visualizer
 
SOMClustering
Self-Organizing Maps algorithm
Version: 2 		Clustering
 
SVM
Classify samples using SVM
Version: 4 		Prediction
 
SelectFeaturesColumns
Takes a 'column slice' from a .res, .gct, .snp, .cn, .loh, .odf, or .cls file.
Version: 4 		Gene List Selection
 
SelectFeaturesRows
Generate a .res, .gct, .snp, .cn, .loh, or .odf file containing only specified features (i.e. rows).
Version: 4 		Gene List Selection
 
SnpViewer
Displays a heat map of snp data
Version: 3 		Visualizer
 
SplitDatasetTrainTest
Splits a dataset (and cls file) into a number of train and test subsets
Version: 3 		Preprocess & Utilities
 
SubMap
Maps subclasses between two data sets
Version: 1 		Clustering
 
SubMapBrowser
Surveys all possible subclass mappings
Version: 1 		Clustering
 
SurvivalCurve
Draws a survival curve based on a cls file
Version: 1 		Survival Analysis
 
SurvivalDifference
Tests for survival difference based on cls file
Version: 1 		Survival Analysis
 
TransposeDataset
Transpose a Dataset - .res .gct, .odf
Version: 3 		Preprocess & Utilities
 
UniquifyLabels
Makes row and column labels unique
Version: 1 		Preprocess & Utilities
 
VennDiagram
Displays a Venn diagram
Version: 1 		Visualizer
 
WeightedVoting
Weighted Voting classification
Version: 3 		Prediction
 
WeightedVotingXValidation
Weighted Voting classification with Leave-One-Out Cross-Validation
Version: 3 		Prediction
 
XChromosomeCorrect
Corrects X Chromosome SNP's for male samples.
Version: 3 		SNP Analysis
 
caArrayImportViewer
A visualizer to import data from caArray into GenePattern via the mage-om api
Version: 1 		Visualizer
 
mzXMLToCsv
Converts a mzXML file to a zip of csv files
Version: 1 		Proteomics