GenePattern Modules


Click the Html or Pdf icons to view a module's documentation.

Modules in the repository can be installed on a local GenePattern server. Most of these modules are also installed on the public GenePattern server.

View by Category:

NameTypeAvailability
ApplyGatingML
Apply a Gating-ML file on an FCS data file (gate and/or transform list mode data)
Pdf  Version: 1
Flow Cytometry * Public Server Only
Arff2Gct
Convert an .arff file into a GenePattern .gct / .cls file pair
Pdf  Version: 0.4
Preprocess & Utilities * Public Server Only
Beroukhim.Getz.2007.PNAS.Glioma.GISTIC
GISTIC pipeline
Html  Version: 1
pipeline * Public Server Only
Birdseed
SNP genotyping algorithm that runs on the Affymetrix 500K, SNP5.0, and SNP6.0 platforms
Pdf  Version: 1
SNP Analysis * Public Server Only
BirdseedCallRate
Computes the call rate of the Birdseed algorithm.
Pdf  Version: 1
SNP Analysis * Public Server Only
BirdseedDataPreparation
Creates a set of BSNP files from a SNP file
Pdf  Version: 1
SNP Analysis * Public Server Only
BlastTrainTest
Sequence similarity prediction using BLAST
Pdf  Version: 0.4
Prediction * Public Server Only
BlastXValidation
Sequence similarity cross-validation prediction using BLAST
Pdf  Version: 0.5
Prediction * Public Server Only
CBS
Segments DNA copy number data into regions of estimated equal copy number using circular binary segmentation (CBS).
Pdf  Version: 2
SNP Analysis * Public Server Only
COPA
Perform Cancer Outlier Profile Analysis (COPA)
Pdf  Version: 1
Gene List Selection * Public Server Only
ComBat
Performs batch correction on a dataset containing multiple batches
Html  Version: 3
Preprocess & Utilities * Public Server Only
CombineOdf
Combine two prediction results files into a single, weighted, multi-label prediction results file
Pdf  Version: 0.4
Preprocess & Utilities * Public Server Only
CompensateFCS
Compensates an FCS data file
Pdf  Version: 1
Flow Cytometry * Public Server Only
CopyNumberInference
Infers copy number from probe intensity values
Pdf  Version: 1
SNP Analysis * Public Server Only
CopyNumberInferencePipeline.Part1of2
First part of the CopyNumberInferencePipeline
Pdf  Version: 1
pipeline * Public Server Only
CopyNumberInferencePipeline
Generates segmented copy number calls from raw tumor and normal SNP6 CEL files
Pdf  Version: 1
pipeline * Public Server Only
CopyNumberNoise
Measures noise, calculates QC metrics on copy number data.
Pdf  Version: 1
SNP Analysis * Public Server Only
ESPPredictor
Determine which tryptic peptides will generate the highest signal in ESI-MS
Pdf  Version: 1
Proteomics * Public Server Only
ExpressionFileCreator
Creates a RES or GCT file from a set of Affymetrix CEL files
Pdf  Version: 11
Preprocess & Utilities * Public Server Only
FCMFeatureExtraction
Calculation of features from clustered flow cytometry data.
Pdf  Version: 1
Flow Cytometry * Public Server Only
FCMSinglePanelQC
Single panel flow cytometry data quality control
Pdf  Version: 1
Flow Cytometry * Public Server Only
FCSNormalization
Per-channel basis normalization of flow cytometry data.
Pdf  Version: 1
Flow Cytometry * Public Server Only
FLAMEChooseOptimalClusterNumber
Determine the optimal number of clusters for each sample based on the range of cluster numbers provided to FLAMEMixtureModel.
Pdf  Version: 4
FLAME * Public Server Only
FLAMEContourDataGenerator
Generate data which allows the FLAMEViewer to draw a 3-D contour plot of the clusters in the sample.
Pdf  Version: 1
FLAME * Public Server Only
FLAMEContourViewer.Pipeline
Run the FLAMEContourDataGenerator and FLAMEViewer modules. Using the pipeline is more convenient than running the two modules individually.
Html  Version: 1
pipeline * Public Server Only
FLAMEMetacluster
Take the data samples, which have been optimally clustered into subpopulations, and match the subpopulations so that a given population can be identified uniformly across all samples.
Pdf  Version: 4
FLAME * Public Server Only
FLAMEMixtureModel
Cluster each preprocessed sample data file over a range of possible cluster numbers.
Pdf  Version: 4
FLAME * Public Server Only
FLAMEPreprocess
Perform a series of preprocessing operations on flow cytometric data files, including column/channel selection, bi-exponential transformation, and optional live-cell gating.
Pdf  Version: 4
FLAME * Public Server Only
FLAMEPreviewTransformation
Evaluate data transformations based on one representative sample.
Pdf  Version: 2
FLAME * Public Server Only
FLAMEViewer
Display a 3-D scatterplot and, if FLAMEContourDataGenerator was run, a 3-D contour plot of the clusters in the sample.
Pdf  Version: 1
Visualizer * Public Server Only
FlowClustClassifyFCS
Classify flow cytometry data using the FlowClust algorithm.
Pdf  Version: 1
Flow Cytometry * Public Server Only
FlowFingerprinting
Takes a flow set and generates a description of the multivariate probability distribution function of its flow cytometry data in the form of a fingerprint
Pdf  Version: 1
Flow Cytometry * Public Server Only
FlowMeansCluster
Cluster flow cytometry data using the FlowMeans algorithm.
Pdf  Version: 1
Flow Cytometry * Public Server Only
FlowMergeCluster
Cluster flow cytometry data using FlowMerge.
Pdf  Version: 1
Flow Cytometry * Public Server Only
GISTIC_2.0
Genomic Identification of Significant Targets in Cancer
Pdf  Version: 5
SNP Analysis * Public Server Only
Gct2Arff
Convert a GenePattern .gct / .cls file pair into an .arff file
Pdf  Version: 0.3
Preprocess & Utilities * Public Server Only
IlluminaConcatenator
Concatenate normalized Illumina probe sets into a single GCT file
Pdf  Version: 1
Preprocess & Utilities * Public Server Only
IlluminaDASLPipeline
Create a GenePattern gct file from raw Illumina scan data (comprises IlluminaScanExtractor, IlluminaNormalizer, and IlluminaConcatenator)
Pdf  Version: 1
pipeline * Public Server Only
IlluminaNormalizer
Normalize zipped Illumina scans
Pdf  Version: 1
Preprocess & Utilities * Public Server Only
IlluminaScanExtractor
Extract intensity values from Illumina scans
Pdf  Version: 1
Preprocess & Utilities * Public Server Only
ImmPortCSV2TXT
Convert a .csv file to a .txt file that FLOCK can read
Html  Version: 1
Flow Cytometry * Public Server Only
ImmPortColSelection
Select a set of columns from a txt file
Html  Version: 1
Flow Cytometry * Public Server Only
ImmPortCrossSample
Applying an individual FLOCK result across another FCM sample (.txt) version 1 (1-round Kmeans)
Html  Version: 1
Flow Cytometry * Public Server Only
ImmPortFCSConvLogicleTrans
Logicle transformation of an fcs file to .txt file
Html  Version: 1
Flow Cytometry * Public Server Only
ImmPortFLOCK
Automated Gating with ImmPort FLOCK algorithm
Html  Version: 1
Flow Cytometry * Public Server Only
InsertGenomicLocations
Inserts genomic locations into the output file from RemoveGenomicLocations
Pdf  Version: 1
SNP Analysis * Public Server Only
KMeansClassifyFCS
Find clusters in a flow cytometry file with k means clustering
Pdf  Version: 1
Flow Cytometry * Public Server Only
MClustClusterLabel
Model based labeling/matching of clusters (mate-clustering)
Pdf  Version: 1
Flow Cytometry * Public Server Only
MClustClusterLabelBIC
Bayesian information criterion (BIC) for model based labeling/matching of clusters; helps estimating the number of labels for MClustClusterLabel.
Pdf  Version: 1
Flow Cytometry * Public Server Only
ModEcocTrainTest
Modified error correcting output code prediction
Pdf  Version: 0.5
Prediction * Public Server Only
ModEcocXValidation
Modified error correcting output code cross-validation prediction
Pdf  Version: 0.3
Prediction * Public Server Only
MutSigCV
Identifies genes that are significantly mutated in cancer genomes, using a model with mutational covariates.
Html  Version: 1
MutSig * Public Server Only
NearestTemplatePrediction
Nearest neighbor prediction based on a list of marker genes.
Pdf  Version: 3
Prediction * Public Server Only
ParallelCBS
Runs CBS algorithm on multiple samples in parallel
Pdf  Version: 1
SNP Analysis * Public Server Only
PlateQAFCS
Look for consistency between wells of a single plate by computing summary statistics.
Pdf  Version: 1
Flow Cytometry * Public Server Only
ProteinDatasetCreation
Extract features from protein .FASTA files for use with standard prediction algorithms
Pdf  Version: 0.4
Preprocess & Utilities * Public Server Only
QuaSAR
A suite of tools for QC, analysis and visualization of data from MRM-MS experiments including assay configuration, calibration curves and new sample analysis.
Pdf  Version: 1
Proteomics * Public Server Only
RankNormalize
Normalize the rows in a data set by rank
Pdf  Version: 1
Statistical Methods * Public Server Only
RemoveCopyNumberOutliers
Reads rows of a copynumber file and removes outliers on a sample-by-sample basis.
Pdf  Version: 1
SNP Analysis * Public Server Only
SNPFileCreator_SNP6
Performs normalization and probe-level summarization to generate a SNP file for a set of Affymetrix SNP 6.0 chip CEL files.
Pdf  Version: 1
SNP Analysis * Public Server Only
SamSPECTRALClusterFCS
Cluster flow cytometry data using the SamSPECTRAL algorithm.
Pdf  Version: 1
Flow Cytometry * Public Server Only
SuggestNumberOfPopulationsFCS
The FlowClust module requires that you specify how many populations you are looking for. This module takes a data driven approach and attempts to discover how many populations are present in an FCS file
Pdf  Version: 1
Flow Cytometry * Public Server Only
SurvivalCurve
Draws a survival curve based on a cls file
Pdf  Version: 3
Survival Analysis * Public Server Only
TangentNormalization
Applies tangent normalization to copy number data
Pdf  Version: 1
SNP Analysis * Public Server Only
ABasicModule
This is a basic GenePattern module written in Python 3. It can be taken as a "blank canvas" for future modules. It reads a file and potentially adds a
Html  Version: 1
Administration Module Repository
ABSOLUTE.review
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Extracts the absolute copy number per cancer cell from a mixed DNA population. Use this module for the Review and Extract step in the workflow (after ABSOLUTE).
Html  Version: 1.4
SNP Analysis Module Repository
ABSOLUTE.summarize
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Summarizes the results from multiple ABSOLUTE runs so that an analyst can manually review the solutions.
Html  Version: 1.4
SNP Analysis Module Repository
ABSOLUTE
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Extracts absolute copy numbers per cancer cell from a mixed DNA population. Use this module for the per-sample processing step in the workflow (usually after HAPSEG).
Html  Version: 1.5
SNP Analysis Module Repository
AddFCSEventIndex
Adds indexes to events in a Flow Cytometry Standard (FCS) data file.
Pdf  Version: 2
Flow Cytometry Module Repository
AddFCSParameter
Add parameters and their values to a FCS data file
Pdf  Version: 2
Flow Cytometry Module Repository
AddNoiseToFCS
Add noise to specified parameters in an FCS data file.
Pdf  Version: 2
Flow Cytometry Module Repository
AddOrReplaceReadGroups
Replaces all read groups in the input file with a new read group and assigns all reads to this read group in the output
Pdf  Version: 1
Preprocess & Utilities Module Repository
AffySTExpressionFileCreator
[Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Creates a GCT file from a set of CEL files from Affymetrix ST arrays.
Html  Version: 0.14
Preprocess & Utilities Module Repository
ARACNE
Runs the ARACNE algorithm for reverse engineering cellular networks
Pdf  Version: 2
Pathway Analysis Module Repository
AreaChange
Calculates fraction of area under the spectrum that is attributable to signal (area after noise removal / original area)
Pdf  Version: 2
Proteomics Module Repository
AuDIT
Automated Detection of Inaccurate and Imprecise Transitions in MRM Mass Spectrometry
Html  Version: 6
Proteomics Module Repository
BamToSam
Converts a BAM file to a SAM file
Pdf  Version: 1
Data Format Conversion Module Repository
BedToGtf
Converts BED files to GFF or GTF format
Pdf  Version: 1
Data Format Conversion Module Repository
Beroukhim.Getz.2007.PNAS.Glioma.GISTIC
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots based on a single user-specified gene.
Red x  Version: 2
pipeline Module Repository
BlastSubtraction
For the PathSeq pipeline, scatter a BlastSubtraction for each input fq1 file
Html  Version: 16
pipeline Module Repository
Bowtie.aligner
Bowtie2 (v. 2.1.0) is an ultrafast and memory-efficient short read aligner.
Html  Version: 4
RNA-seq Module Repository
Bowtie.indexer
Builds a Bowtie2 (v. 2.1.0) index from a set of DNA sequences
Html  Version: 2
RNA-seq Module Repository
BWA.aln
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] A fast and accurate short-read alignment tool that allows for mismatches and gaps. Alignments are output in a SAM format file, which provides Phred-scale quality scores for each alignment. Uses BWA 0.7.4 aln and samse/sampe.
Html  Version: 1.19
RNA-seq Module Repository
BWA.bwasw
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Aligns long sequences (>200 bp) to a sequence database using BWA 0.7.4 bwasw.
Html  Version: 1.14
RNA-seq Module Repository
BWA.indexer
Creates a BWT index from a sequence FASTA file
Pdf  Version: 1
RNA-seq Module Repository
CART
Classification and Regression Tree
Pdf  Version: 2
Prediction Module Repository
CARTXValidation
Classification and Regression Tree X-Validation
Pdf  Version: 2
Prediction Module Repository
CBS
Segments DNA copy number data into regions of estimated equal copy number using circular binary segmentation (CBS).
Html  Version: 3
SNP Analysis Module Repository
CBSWrapperPipeline
A one step pipeline that runs CBS
Pdf  Version: 2
pipeline Module Repository
ClassNeighbors
Select genes that most closely resemble a profile
Pdf  Version: 1
Gene List Selection Module Repository
ClsFileCreator
A tool to create a class label (CLS) file.
Html  Version: 4
javascript Module Repository
CNToXCN

Pdf  Version: 1
SNP Analysis Module Repository
CollapseDataset
Collapses all probe set values for a gene into a single vector of values
Pdf  Version: 1
Preprocess & Utilities Module Repository
ComBat
Batch Correction
Html  Version: 3
Preprocess & Utilities Module Repository
ComparativeMarkerSelection
Identify differentially expressed genes that can discriminate between distinct classes of samples.
Html  Version: 10
Gene List Selection Module Repository
ComparativeMarkerSelectionViewer
Views the results from ComparativeMarkerSelection
Html  Version: 9
javascript Module Repository
CompareSpectra
Compares two spectra to determine similarity
Pdf  Version: 3
Proteomics Module Repository
ConcatenateFilelist
Concatenate all of the items in the input filelist into a single large file.
Pdf  Version: 1
Preprocess & Utilities Module Repository
ConsensusClustering
Resampling-based clustering method
Pdf  Version: 7.2
Clustering Module Repository
ConvertLineEndings
Converts line endings to the host operating system's format.
Pdf  Version: 2
Preprocess & Utilities Module Repository
ConvertToMAGEML
Converts a gct, res, or odf dataset file to a MAGE-ML file
Pdf  Version: 2
Preprocess & Utilities Module Repository
ConvertToMAGETAB
A module to export data from GenePattern in MAGE-TAB format
Pdf  Version: 2
Preprocess & Utilities Module Repository
COPA
Performs Cancer Outlier Profile Analysis (COPA)
Pdf  Version: 1
Gene List Selection Module Repository
CopyNumberDivideByNormals
Determines the copy number of a target SNP
Pdf  Version: 3
SNP Analysis Module Repository
CopyNumberNoise
Measures noise, calculates QC metrics on copynumber data.
Pdf  Version: 1
SNP Analysis Module Repository
CoxRegression
Cox regression using clinical data and .cls file
Pdf  Version: 1
Survival Analysis Module Repository
CreateSymlinks
Creates symlinks to the input files in the job results directory. This is intended to be a helper module for creating scatter-gather pipelines. Note that this module is not supported on Windows
Html  Version: 1
Preprocess & Utilities Module Repository
CsvToFcs
Converts a Comma separated values (CSV) file to a Flow Cytometry Standard (FCS) file.
Pdf  Version: 2
Data Format Conversion Module Repository
Cuffcompare
Cufflinks 2.0.2 - Cuffcompare - Analyzes the transcribed fragments in an assembly
Html  Version: 8
RNA-seq Module Repository
Cuffdiff
Cufflinks 2.0.2 - Finds significant changes in transcript expression, splicing, and promoter use
Html  Version: 7
RNA-seq Module Repository
Cufflinks.cuffcompare
Cufflinks 2.0.2 - Cuffcompare - Analyzes the transcribed fragments in an assembly
Html  Version: 7
RNA-seq Module Repository
Cufflinks.cuffdiff
Cufflinks 2.0.2 - Finds significant changes in transcript expression, splicing, and promoter use
Html  Version: 6
RNA-seq Module Repository
Cufflinks.cuffmerge
Cufflinks 2.0.2\: Cuffmerge - Merge several Cufflinks assemblies
Html  Version: 2
RNA-seq Module Repository
Cufflinks
Cufflinks 2.0.2 - Assembles transcripts, estimates abundances, and tests for differential expression and regulation in RNA-seq samples
Html  Version: 7
RNA-seq Module Repository
CufflinksCuffmergePipeline
Creates multiple transcript assemblies using Cufflinks and then merges these assemblies into one
Html  Version: 1
pipeline Module Repository
CufflinksWrapperPipeline
A wrapper pipeline containing Cufflinks that is meant to be used as part of a scatter-gather pipeline
Html  Version: 1
pipeline Module Repository
Cuffmerge
Cufflinks 2.0.2\: Cuffmerge - Merge several Cufflinks assemblies
Html  Version: 3
RNA-seq Module Repository
CummeRbund.GeneSetReport
[Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots based on a user-provided list of genes.
Html  Version: 0.21
RNA-seq Module Repository
CummeRbund.QcReport
[Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots and tables related to QC and Global Stats.
Html  Version: 0.30
RNA-seq Module Repository
CummeRbund.SelectedConditionsReport
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots based on a user-provided list of conditions.
Html  Version: 0.11
RNA-seq Module Repository
CummeRbund.SelectedGeneReport
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots based on a single user-specified gene.
Html  Version: 0.17
RNA-seq Module Repository
CytoscapeViewer
Visualizes a gene network
Html  Version: 2
Visualizer Module Repository
DeIdentifyFCS
DeIdentifyFCS an FCS data file; remove keywords from a list or matching a regular expression; useful to anonymize FCS data files and/or to remove specific (e.g., clinical) information
Pdf  Version: 1
Flow Cytometry Module Repository
DESeq2
A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductor
Html  Version: 0.3
Gene List Selection Module Repository
DiSCoVER
Beta implementation of the DiSCoVER algorithm.
Html  Version: 1
Prediction Module Repository
DownloadURL
Downloads a file from a URL
Pdf  Version: 1
Preprocess & Utilities Module Repository
ExpressionFileCreator
Creates a RES or GCT file from a set of Affymetrix CEL files. For IVT arrays only; use AffySTExpressionFileCreator for ST arrays.
Html  Version: 12
Preprocess & Utilities Module Repository
ExprToGct
Converts an EXPR file to GCT format
Pdf  Version: 2
Data Format Conversion Module Repository
ExtractColumnNames
Lists the sample descriptors from a .res file.
Pdf  Version: 2
Preprocess & Utilities Module Repository
ExtractComparativeMarkerResults
Creates a derived dataset and feature list file from the results of ComparativeMarkerSelection
Pdf  Version: 4
Gene List Selection Module Repository
ExtractFCSDataset
Extract one or more FCS datasets from an FCS data file
Pdf  Version: 2
Flow Cytometry Module Repository
ExtractFCSKeywords
Extracts keyword(s) value(s) from a Flow Cytometry Standard (FCS) file.
Pdf  Version: 2
Flow Cytometry Module Repository
ExtractFCSParameters
Extract specified parameters (dimensions) from an FCS data file.
Pdf  Version: 2
Flow Cytometry Module Repository
ExtractRowNames
Extracts the row names from a .res, .gct, or .odf file.
Pdf  Version: 3
Preprocess & Utilities Module Repository
FastQC
Provides quality control metrics on raw sequence data
Html  Version: 1
RNA-seq Module Repository
FastqToSam
Extracts read sequences and qualities from the input fastq file and writes them into the output file in unaligned SAM or BAM format
Pdf  Version: 1
Data Format Conversion Module Repository
FcsToCsv
Converts a Flow Cytometry Standard (FCS) file to a Comma Separated Values (CSV) file.
Pdf  Version: 3
Data Format Conversion Module Repository
FeatureSummaryViewer
Feature Summary Viewer
Pdf  Version: 4
Visualizer Module Repository
FileSplitter
Splits a file into equal-sized chunks, given the number of lines per output file
Pdf  Version: 2
Preprocess & Utilities Module Repository
FilterFilelist
a helper module which generates a filtered filelist from the input filelist and some filter parameters.
Pdf  Version: 1
Preprocess & Utilities Module Repository
FLAMEPreprocess
Performs preprocessing of .fcs or .txt flow cytometric data files
Pdf  Version: 4.1
Flow Cytometry Module Repository
Fpkm_trackingToGct
Takes a Cufflinks FPKM_tracking file and converts it to GCT format.
Pdf  Version: 5
RNA-seq Module Repository
GctToPcl
Convert .gct to .pcl
Pdf  Version: 1
Data Format Conversion Module Repository
GeneListSignificanceViewer
Views the results of marker analysis
Pdf  Version: 4
Visualizer Module Repository
GeneNeighbors
Select genes that most closely resemble a continuous profile (e.g., another gene)
Pdf  Version: 4
Gene List Selection Module Repository
GenePatternDocumentExtractor
Extracts GenePattern pipelines and other embedded GenePattern data from Word 2007 documents created with the Microsoft Word Add-In for the GenePattern Reproducible Research Document.
Pdf  Version: 1
Preprocess & Utilities Module Repository
GEOImporter
Imports data from the Gene Expression Omnibus (GEO)
Pdf  Version: 5
Preprocess & Utilities Module Repository
GISTIC_2.0
Genomic Identification of Significant Targets in Cancer (version 2.0.23)
Html  Version: 6.14
SNP Analysis Module Repository
GLAD
Gain and Loss Analysis of DNA
Pdf  Version: 2
SNP Analysis Module Repository
GlobalAlignment
standard global sequence analysis
Pdf  Version: 0
Sequence Analysis Module Repository
Golub.Slonim.1999.Nature.all.aml.pipeline
ALL/AML methodology, from Golub and Slonim et al., 1999
Pdf  Version: 2
pipeline Module Repository
Golub.Slonim.1999.Science.all.aml.pipeline
ALL/AML methodology, from Golub and Slonim et al., 1999
Pdf  Version: 1
pipeline Module Repository
GSEA
Gene Set Enrichment Analysis
Html  Version: 19.0.18
Gene List Selection Module Repository
GSEALeadingEdgeViewer
Leading Edge Viewer for GSEA results
Html  Version: 5
Visualizer Module Repository
GSEAPreranked
Runs the gene set enrichment analysis against a user-supplied ranked list of genes.
Html  Version: 6.0.10
Gene List Selection Module Repository
HAPSEG
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] A probabilistic method to interpret bi-allelic marker data in cancer samples.
Html  Version: 1.6
SNP Analysis Module Repository
HeatMapImage
Creates a heat map from a dataset
Pdf  Version: 6
Image Creators Module Repository
HeatMapViewer
A configurable heat map viewer that provides users with several options for manipulating and visualizing array-based data
Pdf  Version: 13
Visualizer Module Repository
HierarchicalClustering.MATLAB
Hierarchical Clustering
Pdf  Version: 0
Clustering Module Repository
HierarchicalClustering
Perform hierarchical clustering on samples (columns) or/and genes (rows).
Html  Version: 7.14
Clustering Module Repository
HierarchicalClusteringImage.MATLAB
Hierarchical Clustering Image
Pdf  Version: 2
Image Creators Module Repository
HierarchicalClusteringImage
Creates an image of the dendrogram generated from HierarchicalClustering
Pdf  Version: 4
Image Creators Module Repository
HierarchicalClusteringViewer
Views results of hierarchical clustering.
Pdf  Version: 11
Visualizer Module Repository
Hisat2Aligner
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).
Html  Version: 1
Sequence Analysis Module Repository
Hisat2Indexer
Indexes one or more Fasta files for use in the Hisat2Aligner.
Html  Version: 1
RNA-Seq Module Repository
Hu68kHu35kAtoU95
Converts a list of Affymetrix Hu6800/Hu35KsubA probes to the corresponding Affymetrix U95Av2 probes.
Pdf  Version: 1
Preprocess & Utilities Module Repository
igv.js
Launches igv.js with input file(s)
Html  Version: 1
javascript Module Repository
IGV
Launches IGV with input file(s)
Html  Version: 5
IGV Module Repository
IlluminaExpressionFileCreator
Creates a GCT file from a zip of Illumina IDAT files and an Illumina manifest file
Pdf  Version: 2
Preprocess & Utilities Module Repository
ImputeMissingValues.KNN
Imputes missing values
Pdf  Version: 13
Missing Value Imputation Module Repository
ImputeMissingValuesKNN
Imputes missing values
Pdf  Version: 13
Missing Value Imputation Module Repository
InstallRPackages_R2.15
Installs packages into the GenePattern R-2.15 site library
Html  Version: 0.2
Administration Module Repository
InstallRPackages_R3.0
Installs packages into the GenePattern R-3.0 site library
Html  Version: 0.1
Administration Module Repository
InstallRPackages_R3.1
Installs packages into the GenePattern R-3.1 site library
Html  Version: 0.1
Administration Module Repository
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
Pdf  Version: 2
Visualizer Module Repository
Kallisto
Running Kallisto with basic parameters to perfomr pseudoalignment using a human transcriptome index (GRCh 38 from the Ensembl Archive Release 95).
Html  Version: 1
RNA-Seq Module Repository
KMeansClustering
Module that performs the K-Means Clustering algorithm
Pdf  Version: 2
Clustering Module Repository
KNN
K-nearest neighbors classification
Pdf  Version: 4
Prediction Module Repository
KNNXValidation
KNN classification with Leave-One-Out Cross-Validation
Pdf  Version: 6
Prediction Module Repository
KSscore
Computes the Kolmogorov-Smirnov score for a set of genes within an ordered list.
Pdf  Version: 1
Statistical Methods Module Repository
LandmarkMatch
A proteomics method to propogate identifed peptides across multiple MS runs
Pdf  Version: 2
Proteomics Module Repository
ListFiles
a helper module which outputs a filelist, the list of all files in the input directory, similar to the unix 'ls' command
Red x  Version: 0.3
Preprocess & Utilities Module Repository
LocatePeaks
Locates detected peaks in a spectrum.
Pdf  Version: 2
Proteomics Module Repository
LogicleTransformFCS
Logicle transformation of (selected) parameters in a list mode FCS data file.
Pdf  Version: 1
Flow Cytometry Module Repository
LogisticRegression
Logistic regression using clinical data and .cls file
Pdf  Version: 1
Survival Analysis Module Repository
LOHPaired
Computes LOH for paired samples
Pdf  Version: 3
SNP Analysis Module Repository
Lu.Getz.Miska.Nature.June.2005.clustering.ALL.pipeline
Hierarchical clustering of 73 ALL samples with various types of genetic alterations
Pdf  Version: 0
pipeline Module Repository
Lu.Getz.Miska.Nature.June.2005.clustering.ep.miRNA.pipeline
Hierarchical clustering of 89 epithelial samples in miRNA space.
Pdf  Version: 0
pipeline Module Repository
Lu.Getz.Miska.Nature.June.2005.clustering.ep.mRNA.pipeline
Hierarchical clustering of 89 epithelial samples in mRNA space
Pdf  Version: 0
pipeline Module Repository
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
Pdf  Version: 0
pipeline Module Repository
Lu.Getz.Miska.Nature.June.2005.mouse.lung.pipeline
Normal/tumor classifier and kNN prediction of mouse lung samples
Pdf  Version: 0
pipeline Module Repository
Lu.Getz.Miska.Nature.June.2005.mouse.lung.pipeline
Normal/tumor classifier and kNN prediction of mouse lung samples
Pdf  Version: 1
pipeline Module Repository
Lu.Getz.Miska.Nature.June.2005.PDT.miRNA.pipeline
PNN Prediction using mRNA
Pdf  Version: 1
pipeline Module Repository
Lu.Getz.Miska.Nature.June.2005.PDT.mRNA.pipeline
PNN Prediction using mRNA
Pdf  Version: 1
pipeline Module Repository
MAGEMLImportViewer
A visualizer to import data in MAGE-ML format into GenePattern
Pdf  Version: 2
Visualizer Module Repository
MAGETABImportViewer
A visualizer to import data in MAGE-TAB format into GenePattern
Pdf  Version: 2
Visualizer Module Repository
MapChipFeaturesGeneral
Change (map) the features (genes) of a dataset
Pdf  Version: 3
Preprocess & Utilities Module Repository
MergeColumns
Merge datasets by column.
Pdf  Version: 1
Preprocess & Utilities Module Repository
MergeFCSDataFiles
Merge multiple FCS data files into a single FCS datasets; includes multimple subsampling options.
Pdf  Version: 1
Flow Cytometry Module Repository
MergeHTSeqCounts
Merges HTSeq read count data files into one file
Html  Version: 0.4
RNA-seq Module Repository
MergeRows
Merge datasets by row.
Pdf  Version: 1
Preprocess & Utilities Module Repository
MetageneProjection
Projects one or more data sets onto the metagene representation of another data set
Pdf  Version: 1
Projection Module Repository
MINDY
Runs the MINDY algorithm for inferring genes that modulate the activity of a transcription factor at post-transcriptional levels
Pdf  Version: 2
Pathway Analysis Module Repository
MINDYViewer
Visualizes the results of MINDY
Pdf  Version: 1
Visualizer Module Repository
Multiplot
Creates customizable plots of expression data-derived data.
Html  Version: 2
Visualizer Module Repository
MultiplotExtractor
Creates customizable plots of expression data-derived data.
Pdf  Version: 1
Visualizer Module Repository
MutPanning
MutPanning identifies driver genes based on their abundance of nonsynonymous mutations and their increased number of mutations in unusual nucleotide contexts that deviate from the background mutational process.
Html  Version: 2
Mutational Significance Analysis Module Repository
MutSigCV
Identifies genes that are significantly mutated in cancer genomes, using a model with mutational covariates.
Html  Version: 1.2
MutSig Module Repository
mzXMLToCsv
Converts a mzXML file to a zip of csv files
Pdf  Version: 1
Proteomics Module Repository
NMF
Non-negative Matrix Factorization
Pdf  Version: 2
Projection Module Repository
NMFConsensus
Non-negative Matrix Factorization (NMF) Consensus Clustering
Pdf  Version: 5
Clustering Module Repository
ParallelCBS
Runs CBS algorithm on multiple samples in parallel
Pdf  Version: 1
pipeline Module Repository
PCA
Principal Component Analysis (adapted from MeV, http\://www.tm4.org/m)
Pdf  Version: 4
Projection Module Repository
PCAViewer
Principal Component Analysis Visualizer (adapted from MeV, http\://www.tigr.org/software/tm4/mev.html)
Pdf  Version: 6
Visualizer Module Repository
PclToGct
Convert Stanford preclustering file (.pcl) to .gct
Pdf  Version: 1
Data Format Conversion Module Repository
PeakMatch
Perform peak matching on LC-MS data
Pdf  Version: 2
Proteomics Module Repository
Peaks
Determine peaks in the spectrum using a series of digital filters.
Pdf  Version: 2
Proteomics Module Repository
Picard.AddOrReplaceReadGroups
Replaces all read groups in the input file with a new read group and assigns all reads to this read group in the output
Pdf  Version: 3
Preprocess & Utilities Module Repository
Picard.BamToSam
Converts a BAM file to a SAM file
Pdf  Version: 2
Data Format Conversion Module Repository
Picard.CreateSequenceDictionary
Reads FASTA or FASTA.GZ files containing reference sequences, and writes them as a SAM file containing a sequence dictionary
Pdf  Version: 1
Preprocess & Utilities Module Repository
Picard.FastqToSam
Extracts read sequences and qualities from the input fastq file and writes them into the output file in unaligned SAM or BAM format
Pdf  Version: 2
Data Format Conversion Module Repository
Picard.MarkDuplicates
Examines aligned records in the supplied SAM or BAM file to locate duplicate reads.
Pdf  Version: 2
Preprocess & Utilities Module Repository
Picard.ReorderSam
Reorders a SAM file or a BAM file to match contig ordering in a provided reference file
Pdf  Version: 1
Preprocess & Utilities Module Repository
Picard.SamToBam
Converts a SAM file to a BAM file
Pdf  Version: 2
Data Format Conversion Module Repository
Picard.SamToFastq
Convert SAM or BAM files to FASTQ format
Html  Version: 3
Data Format Conversion Module Repository
Picard.SortSam
Sorts a SAM or BAM file in a specified order
Pdf  Version: 4
Preprocess & Utilities Module Repository
Picard.SortSam
Sorts a SAM or BAM file in a specified order, indexes BAM files, and interconverts SAM and BAM files.
Html  Version: 4
Preprocess & Utilities * Public Server Only
PlotPeaks
Plot peaks
Pdf  Version: 2
Proteomics Module Repository
PNN
Probabilistic Neural Network (PNN)
Pdf  Version: 1
Prediction Module Repository
PNNXValidationOptimization
PNN Leave-One-Out Cross-Validation Optimization
Pdf  Version: 2
Prediction Module Repository
PredictionResultsViewer
Visualizes prediction results
Pdf  Version: 4
Visualizer Module Repository
PreprocessDataset
Performs several preprocessing steps on a res, gct, or odf input file
Html  Version: 5
Preprocess & Utilities Module Repository
PreprocessReadCounts
Preprocess RNA-Seq count data in a GCT file so that it is suitable for use in GenePattern analyses.
Html  Version: 0.6
Preprocess & Utilities Module Repository
PreviewFCS
Allows viewing of structural metadata, parameters, and descriptive statistics from a Flow Cytometry Standard (FCS) data file
Pdf  Version: 2
Flow Cytometry Module Repository
ProteoArray
LC-MS proteomic data processing module
Pdf  Version: 1
Proteomics Module Repository
ProteomicsAnalysis
Runs the proteomics analysis on the set of input spectra
Pdf  Version: 2
Proteomics Module Repository
QuaSAR
A suite of tools for QC, analysis and visualization of data from MRM-MS experiments including assay configuration, calibration curves and new sample analysis.
Pdf  Version: 1
Proteomics Module Repository
RankNormalize
Normalize the rows in a data set by rank
Html  Version: 1.9
Statistical Methods Module Repository
Read_group_trackingToGct
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Converts a Cufflinks read_group_tracking file into GCT format
Html  Version: 0.15
RNA-seq Module Repository
RemoveMissingValues
Removes features and/or samples containing missing (NA) values
Pdf  Version: 1
Missing Value Imputation Module Repository
RemoveSaturatedFCSEvents
Remove saturated events from an FCS data file
Pdf  Version: 1
Flow Cytometry Module Repository
RenameFile
Creates a result file with the contents of the input but with a new name. Where possible, this is done without copying the file but instead by simply making a link. While it is possible to run this with a submitted file, the common use will be to change the name of a result file or a previously uploaded file. Note that the original file will still be present in its original location.
Html  Version: 1
Preprocess & Utilities Module Repository
ReorderByClass
Reorder the samples in an expression dataset and class file by class
Pdf  Version: 3
Preprocess & Utilities Module Repository
RNASeQC
Calculates metrics on aligned RNA-seq data.
Pdf  Version: 2
RNA-seq Module Repository
RNAseqMetrics
Calculates metrics on aligned RNA-seq data.
Pdf  Version: 1
RNA-seq Module Repository
SamToBam
Converts a SAM file to a BAM file
Pdf  Version: 1
Data Format Conversion Module Repository
SamToFastq
Convert SAM or BAM files to FASTQ format
Pdf  Version: 1
Data Format Conversion Module Repository
SAMtools.FastaIndex
Indexes a reference sequence in FASTA format
Html  Version: 2
Preprocess & Utilities Module Repository
ScatterBlastSubtraction
For the PathSeq pipeline, scatter a BWASubtraction job for each input fq1 file
Html  Version: 8
pipeline Module Repository
Scripture
Segmentation-based transcript reconstruction algorithm
Pdf  Version: 1
RNA-seq Module Repository
ScripturePipeline
Segmentation-based transcript reconstruction using single- or paired-end reads
Pdf  Version: 3
pipeline Module Repository
ScripturePrealigned
Segmentation-based transcript reconstruction using pre-aligned reads
Pdf  Version: 2
pipeline Module Repository
SegmentationCount
Counts the number of segments in a SEG file.
Pdf  Version: 1
SNP Analysis Module Repository
SelectFeaturesColumns
Takes a 'column slice' from a .res, .gct, .snp, .cn, .loh, .odf, or .cls file.
Pdf  Version: 4
Gene List Selection Module Repository
SelectFeaturesRows
Generate a .res, .gct, .snp, .cn, .loh, or .odf file containing only specified features (i.e. rows).
Pdf  Version: 4
Gene List Selection Module Repository
SelectFileMatrix
A helper module which selects a matrix out of a delimited text file.
Pdf  Version: 1
Preprocess & Utilities Module Repository
SetFCSKeywords
Sets keyword/value(s) in a Flow Cytometry Standard (FCS) file.
Pdf  Version: 2
Flow Cytometry Module Repository
SNPFileCreator
Process Affymetrix SNP probe-level data into an expression value
Pdf  Version: 1
SNP Analysis Module Repository
SNPFileSorter
Sorts a .snp file by Chromosome and location
Pdf  Version: 1
SNP Analysis Module Repository
SNPMultipleSampleAnalysis
Determine Regions of Concordant Copy Number Aberrations
Pdf  Version:
SNP Analysis Module Repository
SnpViewer
Displays a heat map of snp data
Pdf  Version: 3
Visualizer Module Repository
SOMClustering
Self-Organizing Maps algorithm
Pdf  Version: 2
Clustering Module Repository
SOMClusterViewer
Visualize clusters created with the SOM algorithm
Pdf  Version: 5
Visualizer Module Repository
SortSam
Sorts a SAM or BAM file in a specified order
Pdf  Version: 3
Preprocess & Utilities Module Repository
SparseHierarchicalClustering
Cluster the samples in a data matrix using an adaptively-chosen subset of the features.
Pdf  Version: 1
Clustering Module Repository
SplitColumns
Creates a separate file for each column specified from the input file
Pdf  Version: 1
Preprocess & Utilities Module Repository
SplitDatasetTrainTest
Splits a dataset (and cls file) into a number of train and test subsets
Pdf  Version: 4
Preprocess & Utilities Module Repository
SraToFastQ
Converts data in SRA format to FastQ using the SRAToolkit version 2.3.5-2.
Html  Version: 1
RNA-seq Module Repository
ssGSEAProjection
Performs single sample GSEA Projection
Html  Version: 9.1.1
Projection Module Repository
StrandSpecRNAseqEval
Evaluates strand-specific yeast (S. cerevisiae) RNA-seq libraries
Pdf  Version: 1
RNA-seq Module Repository
SubMap
Maps subclasses between two data sets
Pdf  Version: 3
Clustering Module Repository
SubMapBrowser
Surveys all possible subclass mappings
Pdf  Version: 2
Clustering Module Repository
SurvivalCurve
Draws a survival curve based on a cls file
Pdf  Version: 2
Survival Analysis Module Repository
SurvivalDifference
Tests for survival difference based on cls file
Pdf  Version: 1
Survival Analysis Module Repository
SVM
Classify samples using SVM
Pdf  Version: 4
Prediction Module Repository
TCGAImporter
This module imports data from TCGA by taking in a GDC manifest file, downloading the files listed on that manifest, renaming them to be human-friendly, and compiling them into a GCT file to be computer-friendly.
Html  Version: 5
Data Format Conversion Module Repository
TmapToGct
Converts a TMAP file to GCT format
Pdf  Version: 1
Data Format Conversion Module Repository
TopHat
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] TopHat 2.0.11 is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Html  Version: 8.11
RNA-seq Module Repository
TransposeDataset
Transpose a Dataset - .res .gct, .odf
Pdf  Version: 3
Preprocess & Utilities Module Repository
Trimmomatic
Provides a variety of options for trimming Illumina FASTQ files of adapter sequences and low-quality reads.
Html  Version: 1.4
RNA-seq Module Repository
txt2odf
This module turns a TXT file into an ODF file which can be used with other GenePattern Modules.
Html  Version: 3
Data Format Conversion Module Repository
UniquifyLabels
Makes row and column labels unique
Pdf  Version: 1
Preprocess & Utilities Module Repository
VennDiagram
Displays a Venn diagram
Pdf  Version: 1
Visualizer Module Repository
VoomNormalize
Preprocess RNA-Seq count data in a GCT file so that it is suitable for use in GenePattern analyses. Formerly called "PreprocessReadCounts"
Html  Version: 0.9
Preprocess & Utilities Module Repository
WeightedVoting
Weighted Voting classification
Pdf  Version: 3
Prediction Module Repository
WeightedVotingXValidation
Weighted Voting classification with Leave-One-Out Cross-Validation
Pdf  Version: 3
Prediction Module Repository
XChromosomeCorrect
Corrects X Chromosome SNP's for male samples.
Pdf  Version: 3
SNP Analysis Module Repository