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
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 against a human genome index.
Html  Version: 0.1
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
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