Click the 
or 
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.
| Name | Type | Availability | ApplyGatingML Apply a Gating-ML file on an FCS data file (gate and/or transform list mode data)
Version: 1 |
Flow Cytometry | * Public Server Only | Arff2Gct Convert an .arff file into a GenePattern .gct / .cls file pair
Version: 0.4 |
Preprocess & Utilities | * Public Server Only | Beroukhim.Getz.2007.PNAS.Glioma.GISTIC GISTIC pipeline
Version: 1 |
pipeline | * Public Server Only | Birdseed SNP genotyping algorithm that runs on the Affymetrix 500K, SNP5.0, and SNP6.0 platforms
Version: 1 |
SNP Analysis | * Public Server Only | BirdseedCallRate Computes the call rate of the Birdseed algorithm.
Version: 1 |
SNP Analysis | * Public Server Only | BirdseedDataPreparation Creates a set of BSNP files from a SNP file
Version: 1 |
SNP Analysis | * Public Server Only | BlastTrainTest Sequence similarity prediction using BLAST
Version: 0.4 |
Prediction | * Public Server Only | BlastXValidation Sequence similarity cross-validation prediction using BLAST
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).
Version: 2 |
SNP Analysis | * Public Server Only | COPA Perform Cancer Outlier Profile Analysis (COPA)
Version: 1 |
Gene List Selection | * Public Server Only | ComBat Performs batch correction on a dataset containing multiple batches
Version: 3 |
Preprocess & Utilities | * Public Server Only | CombineOdf Combine two prediction results files into a single, weighted, multi-label prediction results file
Version: 0.4 |
Preprocess & Utilities | * Public Server Only | CompensateFCS Compensates an FCS data file
Version: 1 |
Flow Cytometry | * Public Server Only | CopyNumberInference Infers copy number from probe intensity values
Version: 1 |
SNP Analysis | * Public Server Only | CopyNumberInferencePipeline.Part1of2 First part of the CopyNumberInferencePipeline
Version: 1 |
pipeline | * Public Server Only | CopyNumberInferencePipeline Generates segmented copy number calls from raw tumor and normal SNP6 CEL files
Version: 1 |
pipeline | * Public Server Only | CopyNumberNoise Measures noise, calculates QC metrics on copy number data.
Version: 1 |
SNP Analysis | * Public Server Only | ESPPredictor Determine which tryptic peptides will generate the highest signal in ESI-MS
Version: 1 |
Proteomics | * Public Server Only | ExpressionFileCreator Creates a RES or GCT file from a set of Affymetrix CEL files
Version: 11 |
Preprocess & Utilities | * Public Server Only | FCMFeatureExtraction Calculation of features from clustered flow cytometry data.
Version: 1 |
Flow Cytometry | * Public Server Only | FCMSinglePanelQC Single panel flow cytometry data quality control
Version: 1 |
Flow Cytometry | * Public Server Only | FCSNormalization Per-channel basis normalization of flow cytometry data.
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.
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.
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.
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.
Version: 4 |
FLAME | * Public Server Only | FLAMEMixtureModel Cluster each preprocessed sample data file over a range of possible cluster numbers.
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.
Version: 4 |
FLAME | * Public Server Only | FLAMEPreviewTransformation Evaluate data transformations based on one representative sample.
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.
Version: 1 |
Visualizer | * Public Server Only | FlowClustClassifyFCS Classify flow cytometry data using the FlowClust algorithm.
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
Version: 1 |
Flow Cytometry | * Public Server Only | FlowMeansCluster Cluster flow cytometry data using the FlowMeans algorithm.
Version: 1 |
Flow Cytometry | * Public Server Only | FlowMergeCluster Cluster flow cytometry data using FlowMerge.
Version: 1 |
Flow Cytometry | * Public Server Only | GISTIC_2.0 Genomic Identification of Significant Targets in Cancer
Version: 5 |
SNP Analysis | * Public Server Only | Gct2Arff Convert a GenePattern .gct / .cls file pair into an .arff file
Version: 0.3 |
Preprocess & Utilities | * Public Server Only | IlluminaConcatenator Concatenate normalized Illumina probe sets into a single GCT file
Version: 1 |
Preprocess & Utilities | * Public Server Only | IlluminaDASLPipeline Create a GenePattern gct file from raw Illumina scan data (comprises IlluminaScanExtractor, IlluminaNormalizer, and IlluminaConcatenator)
Version: 1 |
pipeline | * Public Server Only | IlluminaNormalizer Normalize zipped Illumina scans
Version: 1 |
Preprocess & Utilities | * Public Server Only | IlluminaScanExtractor Extract intensity values from Illumina scans
Version: 1 |
Preprocess & Utilities | * Public Server Only | ImmPortCSV2TXT Convert a .csv file to a .txt file that FLOCK can read
Version: 1 |
Flow Cytometry | * Public Server Only | ImmPortColSelection Select a set of columns from a txt file
Version: 1 |
Flow Cytometry | * Public Server Only | ImmPortCrossSample Applying an individual FLOCK result across another FCM sample (.txt) version 1 (1-round Kmeans)
Version: 1 |
Flow Cytometry | * Public Server Only | ImmPortFCSConvLogicleTrans Logicle transformation of an fcs file to .txt file
Version: 1 |
Flow Cytometry | * Public Server Only | ImmPortFLOCK Automated Gating with ImmPort FLOCK algorithm
Version: 1 |
Flow Cytometry | * Public Server Only | InsertGenomicLocations Inserts genomic locations into the output file from RemoveGenomicLocations
Version: 1 |
SNP Analysis | * Public Server Only | KMeansClassifyFCS Find clusters in a flow cytometry file with k means clustering
Version: 1 |
Flow Cytometry | * Public Server Only | MClustClusterLabel Model based labeling/matching of clusters (mate-clustering)
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.
Version: 1 |
Flow Cytometry | * Public Server Only | ModEcocTrainTest Modified error correcting output code prediction
Version: 0.5 |
Prediction | * Public Server Only | ModEcocXValidation Modified error correcting output code cross-validation prediction
Version: 0.3 |
Prediction | * Public Server Only | MutSigCV Identifies genes that are significantly mutated in cancer genomes, using a model with mutational covariates.
Version: 1 |
MutSig | * Public Server Only | NearestTemplatePrediction Nearest neighbor prediction based on a list of marker genes.
Version: 3 |
Prediction | * Public Server Only | ParallelCBS Runs CBS algorithm on multiple samples in parallel
Version: 1 |
SNP Analysis | * Public Server Only | PlateQAFCS Look for consistency between wells of a single plate by computing summary statistics.
Version: 1 |
Flow Cytometry | * Public Server Only | ProteinDatasetCreation Extract features from protein .FASTA files for use with standard prediction algorithms
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.
Version: 1 |
Proteomics | * Public Server Only | RankNormalize Normalize the rows in a data set by rank
Version: 1 |
Statistical Methods | * Public Server Only | RemoveCopyNumberOutliers Reads rows of a copynumber file and removes outliers on a sample-by-sample basis.
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.
Version: 1 |
SNP Analysis | * Public Server Only | SamSPECTRALClusterFCS Cluster flow cytometry data using the SamSPECTRAL algorithm.
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
Version: 1 |
Flow Cytometry | * Public Server Only | SurvivalCurve Draws a survival curve based on a cls file
Version: 3 |
Survival Analysis | * Public Server Only | TangentNormalization Applies tangent normalization to copy number data
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
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).
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.
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).
Version: 1.5 |
SNP Analysis | Module Repository | AddFCSEventIndex Adds indexes to events in a Flow Cytometry Standard (FCS) data file.
Version: 2 |
Flow Cytometry | Module Repository | AddFCSParameter Add parameters and their values to a FCS data file
Version: 2 |
Flow Cytometry | Module Repository | AddNoiseToFCS Add noise to specified parameters in an FCS data file.
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
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.
Version: 0.14 |
Preprocess & Utilities | Module Repository | ARACNE Runs the ARACNE algorithm for reverse engineering cellular networks
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)
Version: 2 |
Proteomics | Module Repository | AuDIT Automated Detection of Inaccurate and Imprecise Transitions in MRM Mass Spectrometry
Version: 6 |
Proteomics | Module Repository | BamToSam Converts a BAM file to a SAM file
Version: 1 |
Data Format Conversion | Module Repository | BedToGtf Converts BED files to GFF or GTF format
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. 
Version: 2 |
pipeline | Module Repository | BlastSubtraction For the PathSeq pipeline, scatter a BlastSubtraction for each input fq1 file
Version: 16 |
pipeline | Module Repository | Bowtie.aligner Bowtie2 (v. 2.1.0) is an ultrafast and memory-efficient short read aligner.
Version: 4 |
RNA-seq | Module Repository | Bowtie.indexer Builds a Bowtie2 (v. 2.1.0) index from a set of DNA sequences
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.
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.
Version: 1.14 |
RNA-seq | Module Repository | BWA.indexer Creates a BWT index from a sequence FASTA file
Version: 1 |
RNA-seq | Module Repository | CART Classification and Regression Tree
Version: 2 |
Prediction | Module Repository | CARTXValidation Classification and Regression Tree X-Validation
Version: 2 |
Prediction | Module Repository | CBS Segments DNA copy number data into regions of estimated equal copy number using circular binary segmentation (CBS).
Version: 3 |
SNP Analysis | Module Repository | CBSWrapperPipeline A one step pipeline that runs CBS
Version: 2 |
pipeline | Module Repository | CellFie The CellFie analysis
Version: 1.2 |
Pathway Analysis | Module Repository | ClassNeighbors Select genes that most closely resemble a profile
Version: 1 |
Gene List Selection | Module Repository | ClsFileCreator A tool to create a class label (CLS) file.
Version: 4 |
javascript | Module Repository | CNToXCN
Version: 1 |
SNP Analysis | Module Repository | CollapseDataset Collapses all probe set values for a gene into a single vector of values
Version: 1 |
Preprocess & Utilities | Module Repository | ComBat Batch Correction
Version: 3 |
Preprocess & Utilities | Module Repository | ComparativeMarkerSelection Identify differentially expressed genes that can discriminate between distinct classes of samples.
Version: 10 |
Gene List Selection | Module Repository | ComparativeMarkerSelectionViewer Views the results from ComparativeMarkerSelection
Version: 9 |
javascript | Module Repository | CompareSpectra Compares two spectra to determine similarity
Version: 3 |
Proteomics | Module Repository | ConcatenateFilelist Concatenate all of the items in the input filelist into a single large file.
Version: 1 |
Preprocess & Utilities | Module Repository | ConsensusClustering Resampling-based clustering method
Version: 7.2 |
Clustering | Module Repository | ConstellationMap A downstream visualization and analysis tool for gene set enrichment results with interactive web visualizer.
Version: 1.4.10 |
Statistical Methods | Module Repository | ConvertLineEndings Converts line endings to the host operating system's format.
Version: 2 |
Preprocess & Utilities | Module Repository | ConvertToMAGEML Converts a gct, res, or odf dataset file to a MAGE-ML file
Version: 2 |
Preprocess & Utilities | Module Repository | ConvertToMAGETAB A module to export data from GenePattern in MAGE-TAB format
Version: 2 |
Preprocess & Utilities | Module Repository | COPA Performs Cancer Outlier Profile Analysis (COPA)
Version: 1 |
Gene List Selection | Module Repository | CopyNumberDivideByNormals Determines the copy number of a target SNP
Version: 3 |
SNP Analysis | Module Repository | CopyNumberNoise Measures noise, calculates QC metrics on copynumber data.
Version: 1 |
SNP Analysis | Module Repository | CoxRegression Cox regression using clinical data and .cls file
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
Version: 1 |
Preprocess & Utilities | Module Repository | CsvToFcs Converts a Comma separated values (CSV) file to a Flow Cytometry Standard (FCS) file.
Version: 2 |
Data Format Conversion | Module Repository | Cuffcompare Cufflinks 2.0.2 - Cuffcompare - Analyzes the transcribed fragments in an assembly
Version: 8 |
RNA-seq | Module Repository | Cuffdiff Cufflinks 2.0.2 - Finds significant changes in transcript expression, splicing, and promoter use
Version: 7 |
RNA-seq | Module Repository | Cufflinks.cuffcompare Cufflinks 2.0.2 - Cuffcompare - Analyzes the transcribed fragments in an assembly
Version: 7 |
RNA-seq | Module Repository | Cufflinks.cuffdiff Cufflinks 2.0.2 - Finds significant changes in transcript expression, splicing, and promoter use
Version: 6 |
RNA-seq | Module Repository | Cufflinks.cuffmerge Cufflinks 2.0.2\: Cuffmerge - Merge several Cufflinks assemblies
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
Version: 7 |
RNA-seq | Module Repository | CufflinksCuffmergePipeline Creates multiple transcript assemblies using Cufflinks and then merges these assemblies into one
Version: 1 |
pipeline | Module Repository | CufflinksWrapperPipeline A wrapper pipeline containing Cufflinks that is meant to be used as part of a scatter-gather pipeline
Version: 1 |
pipeline | Module Repository | Cuffmerge Cufflinks 2.0.2\: Cuffmerge - Merge several Cufflinks assemblies
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.
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.
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.
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.
Version: 0.17 |
RNA-seq | Module Repository | CytoscapeViewer Visualizes a gene network
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
Version: 1 |
Flow Cytometry | Module Repository | DESeq2 A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductor
Version: 1 |
Differential Expression | Module Repository | DiSCoVER Beta implementation of the DiSCoVER algorithm.
Version: 1 |
Prediction | Module Repository | DownloadURL Downloads a file from a URL
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.
Version: 12 |
Preprocess & Utilities | Module Repository | ExprToGct Converts an EXPR file to GCT format
Version: 2 |
Data Format Conversion | Module Repository | ExtractColumnNames Lists the sample descriptors from a .res file.
Version: 2 |
Preprocess & Utilities | Module Repository | ExtractComparativeMarkerResults Creates a derived dataset and feature list file from the results of ComparativeMarkerSelection
Version: 4 |
Gene List Selection | Module Repository | ExtractFCSDataset Extract one or more FCS datasets from an FCS data file
Version: 2 |
Flow Cytometry | Module Repository | ExtractFCSKeywords Extracts keyword(s) value(s) from a Flow Cytometry Standard (FCS) file.
Version: 2 |
Flow Cytometry | Module Repository | ExtractFCSParameters Extract specified parameters (dimensions) from an FCS data file.
Version: 2 |
Flow Cytometry | Module Repository | ExtractRowNames Extracts the row names from a .res, .gct, or .odf file.
Version: 3 |
Preprocess & Utilities | Module Repository | FastQC Provides quality control metrics on raw sequence data
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
Version: 1 |
Data Format Conversion | Module Repository | FcsToCsv Converts a Flow Cytometry Standard (FCS) file to a Comma Separated Values (CSV) file.
Version: 3 |
Data Format Conversion | Module Repository | FeatureSummaryViewer Feature Summary Viewer
Version: 4 |
Visualizer | Module Repository | FileSplitter Splits a file into equal-sized chunks, given the number of lines per output file
Version: 2 |
Preprocess & Utilities | Module Repository | FilterFilelist a helper module which generates a filtered filelist from the input filelist and some filter parameters.
Version: 1 |
Preprocess & Utilities | Module Repository | FLAMEPreprocess Performs preprocessing of .fcs or .txt flow cytometric data files
Version: 4.1 |
Flow Cytometry | Module Repository | Fpkm_trackingToGct Takes a Cufflinks FPKM_tracking file and converts it to GCT format.
Version: 5 |
RNA-seq | Module Repository | GctToPcl Convert .gct to .pcl
Version: 1 |
Data Format Conversion | Module Repository | GeneListSignificanceViewer Views the results of marker analysis
Version: 4 |
Visualizer | Module Repository | GeneNeighbors Select genes that most closely resemble a continuous profile (e.g., another gene)
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.
Version: 1 |
Preprocess & Utilities | Module Repository | GEOImporter Imports data from the Gene Expression Omnibus (GEO)
Version: 5 |
Preprocess & Utilities | Module Repository | GISTIC_2.0 Genomic Identification of Significant Targets in Cancer (version 2.0.23)
Version: 6.14 |
SNP Analysis | Module Repository | GLAD Gain and Loss Analysis of DNA
Version: 2 |
SNP Analysis | Module Repository | GlobalAlignment standard global sequence analysis
Version: 0 |
Sequence Analysis | Module Repository | Golub.Slonim.1999.Nature.all.aml.pipeline ALL/AML methodology, from Golub and Slonim et al., 1999
Version: 2 |
pipeline | Module Repository | Golub.Slonim.1999.Science.all.aml.pipeline ALL/AML methodology, from Golub and Slonim et al., 1999
Version: 1 |
pipeline | Module Repository | GSEA Gene Set Enrichment Analysis. <strong>If you are using GSEA on RNA-seq data, please read <a href\
Version: 20.0.4 |
Gene List Selection | Module Repository | GSEALeadingEdgeViewer Leading Edge Viewer for GSEA results
Version: 5 |
Visualizer | Module Repository | GSEAPreranked Runs the gene set enrichment analysis against a user-supplied ranked list of genes.
Version: 7.0.3 |
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.
Version: 1.6 |
SNP Analysis | Module Repository | HeatMapImage Creates a heat map from a dataset
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
Version: 13 |
Visualizer | Module Repository | HierarchicalClustering.MATLAB Hierarchical Clustering
Version: 0 |
Clustering | Module Repository | HierarchicalClustering Perform hierarchical clustering on samples (columns) or/and genes (rows).
Version: 7.14 |
Clustering | Module Repository | HierarchicalClusteringImage.MATLAB Hierarchical Clustering Image
Version: 2 |
Image Creators | Module Repository | HierarchicalClusteringImage Creates an image of the dendrogram generated from HierarchicalClustering
Version: 4 |
Image Creators | Module Repository | HierarchicalClusteringViewer Views results of hierarchical clustering.
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).
Version: 1 |
Sequence Analysis | Module Repository | Hisat2Indexer Indexes one or more Fasta files for use in the Hisat2Aligner.
Version: 1 |
RNA-Seq | Module Repository | Hu68kHu35kAtoU95 Converts a list of Affymetrix Hu6800/Hu35KsubA probes to the corresponding Affymetrix U95Av2 probes.
Version: 1 |
Preprocess & Utilities | Module Repository | igv.js Launches igv.js with input file(s)
Version: 2 |
javascript | Module Repository | IGV Launches IGV with input file(s)
Version: 5 |
IGV | Module Repository | IlluminaExpressionFileCreator Creates a GCT file from a zip of Illumina IDAT files and an Illumina manifest file
Version: 2 |
Preprocess & Utilities | Module Repository | ImputeMissingValues.KNN Imputes missing values
Version: 13 |
Missing Value Imputation | Module Repository | ImputeMissingValuesKNN Imputes missing values
Version: 13 |
Missing Value Imputation | Module Repository | InstallRPackages_R2.15 Installs packages into the GenePattern R-2.15 site library
Version: 0.2 |
Administration | Module Repository | InstallRPackages_R3.0 Installs packages into the GenePattern R-3.0 site library
Version: 0.1 |
Administration | Module Repository | InstallRPackages_R3.1 Installs packages into the GenePattern R-3.1 site library
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
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).
Version: 1 |
RNA-Seq | Module Repository | KMeansClustering Module that performs the K-Means Clustering algorithm
Version: 2 |
Clustering | Module Repository | KNN K-nearest neighbors classification
Version: 4 |
Prediction | Module Repository | KNNXValidation KNN classification with Leave-One-Out Cross-Validation
Version: 6 |
Prediction | Module Repository | KSscore Computes the Kolmogorov-Smirnov score for a set of genes within an ordered list.
Version: 1 |
Statistical Methods | Module Repository | LandmarkMatch A proteomics method to propogate identifed peptides across multiple MS runs
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
Version: 0.3 |
Preprocess & Utilities | Module Repository | LocatePeaks Locates detected peaks in a spectrum.
Version: 2 |
Proteomics | Module Repository | LogicleTransformFCS Logicle transformation of (selected) parameters in a list mode FCS data file.
Version: 1 |
Flow Cytometry | Module Repository | LogisticRegression Logistic regression using clinical data and .cls file
Version: 1 |
Survival Analysis | Module Repository | LOHPaired Computes LOH for paired samples
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
Version: 0 |
pipeline | Module Repository | Lu.Getz.Miska.Nature.June.2005.clustering.ep.miRNA.pipeline Hierarchical clustering of 89 epithelial samples in miRNA space.
Version: 0 |
pipeline | Module Repository | Lu.Getz.Miska.Nature.June.2005.clustering.ep.mRNA.pipeline Hierarchical clustering of 89 epithelial samples in mRNA space
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
Version: 0 |
pipeline | Module Repository | Lu.Getz.Miska.Nature.June.2005.mouse.lung.pipeline Normal/tumor classifier and kNN prediction of mouse lung samples
Version: 0 |
pipeline | Module Repository | Lu.Getz.Miska.Nature.June.2005.mouse.lung.pipeline Normal/tumor classifier and kNN prediction of mouse lung samples
Version: 1 |
pipeline | Module Repository | Lu.Getz.Miska.Nature.June.2005.PDT.miRNA.pipeline PNN Prediction using mRNA
Version: 1 |
pipeline | Module Repository | Lu.Getz.Miska.Nature.June.2005.PDT.mRNA.pipeline PNN Prediction using mRNA
Version: 1 |
pipeline | Module Repository | MAGEMLImportViewer A visualizer to import data in MAGE-ML format into GenePattern
Version: 2 |
Visualizer | Module Repository | MAGETABImportViewer A visualizer to import data in MAGE-TAB format into GenePattern
Version: 2 |
Visualizer | Module Repository | MapChipFeaturesGeneral Change (map) the features (genes) of a dataset
Version: 3 |
Preprocess & Utilities | Module Repository | MergeColumns Merge datasets by column.
Version: 1 |
Preprocess & Utilities | Module Repository | MergeFCSDataFiles Merge multiple FCS data files into a single FCS datasets; includes multimple subsampling options.
Version: 1 |
Flow Cytometry | Module Repository | MergeHTSeqCounts Merges HTSeq read count data files into one file
Version: 0.4 |
RNA-seq | Module Repository | MergeRows Merge datasets by row.
Version: 1 |
Preprocess & Utilities | Module Repository | MetageneProjection Projects one or more data sets onto the metagene representation of another data set
Version: 1 |
Projection | Module Repository | MethylationCNVAnalysis Methylation array preprocessing with the minfi R package and copy-number variation analysis with the conumee R package. Compatible with both 450k or EPIC array data.
Version: 2 |
Module Repository | MINDY Runs the MINDY algorithm for inferring genes that modulate the activity of a transcription factor at post-transcriptional levels
Version: 2 |
Pathway Analysis | Module Repository | MINDYViewer Visualizes the results of MINDY
Version: 1 |
Visualizer | Module Repository | Multiplot Creates customizable plots of expression data-derived data.
Version: 2 |
Visualizer | Module Repository | MultiplotExtractor Creates customizable plots of expression data-derived data.
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.
Version: 2 |
Mutational Significance Analysis | Module Repository | MutSigCV Identifies genes that are significantly mutated in cancer genomes, using a model with mutational covariates.
Version: 1.2 |
MutSig | Module Repository | mzXMLToCsv Converts a mzXML file to a zip of csv files
Version: 1 |
Proteomics | Module Repository | NMF Non-negative Matrix Factorization
Version: 2 |
Projection | Module Repository | NMFConsensus Non-negative Matrix Factorization (NMF) Consensus Clustering
Version: 5 |
Clustering | Module Repository | ParallelCBS Runs CBS algorithm on multiple samples in parallel
Version: 1 |
pipeline | Module Repository | PCA Principal Component Analysis (adapted from MeV, http\://www.tm4.org/m)
Version: 4 |
Projection | Module Repository | PCAViewer Principal Component Analysis Visualizer (adapted from MeV, http\://www.tigr.org/software/tm4/mev.html)
Version: 6 |
Visualizer | Module Repository | PclToGct Convert Stanford preclustering file (.pcl) to .gct
Version: 1 |
Data Format Conversion | Module Repository | PeakMatch Perform peak matching on LC-MS data
Version: 2 |
Proteomics | Module Repository | Peaks Determine peaks in the spectrum using a series of digital filters.
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
Version: 3 |
Preprocess & Utilities | Module Repository | Picard.BamToSam Converts a BAM file to a SAM file
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
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
Version: 2 |
Data Format Conversion | Module Repository | Picard.MarkDuplicates Examines aligned records in the supplied SAM or BAM file to locate duplicate reads.
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
Version: 1 |
Preprocess & Utilities | Module Repository | Picard.SamToBam Converts a SAM file to a BAM file
Version: 2 |
Data Format Conversion | Module Repository | Picard.SamToFastq Convert SAM or BAM files to FASTQ format
Version: 3 |
Data Format Conversion | Module Repository | Picard.SortSam Sorts a SAM or BAM file in a specified order
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.
Version: 4 |
Preprocess & Utilities | * Public Server Only | PlotPeaks Plot peaks
Version: 2 |
Proteomics | Module Repository | PNN Probabilistic Neural Network (PNN)
Version: 1 |
Prediction | Module Repository | PNNXValidationOptimization PNN Leave-One-Out Cross-Validation Optimization
Version: 2 |
Prediction | Module Repository | PredictionResultsViewer Visualizes prediction results
Version: 4 |
Visualizer | Module Repository | PreprocessDataset Performs several preprocessing steps on a res, gct, or odf input file
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.
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
Version: 2 |
Flow Cytometry | Module Repository | ProteoArray LC-MS proteomic data processing module
Version: 1 |
Proteomics | Module Repository | ProteomicsAnalysis Runs the proteomics analysis on the set of input spectra
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.
Version: 1 |
Proteomics | Module Repository | RankNormalize Normalize the rows in a data set by rank
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
Version: 0.15 |
RNA-seq | Module Repository | RemoveMissingValues Removes features and/or samples containing missing (NA) values
Version: 1 |
Missing Value Imputation | Module Repository | RemoveSaturatedFCSEvents Remove saturated events from an FCS data file
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.
Version: 1 |
Preprocess & Utilities | Module Repository | ReorderByClass Reorder the samples in an expression dataset and class file by class
Version: 3 |
Preprocess & Utilities | Module Repository | RNASeQC Calculates metrics on aligned RNA-seq data.
Version: 2 |
RNA-seq | Module Repository | RNAseqMetrics Calculates metrics on aligned RNA-seq data.
Version: 1 |
RNA-seq | Module Repository | SamToBam Converts a SAM file to a BAM file
Version: 1 |
Data Format Conversion | Module Repository | SamToFastq Convert SAM or BAM files to FASTQ format
Version: 1 |
Data Format Conversion | Module Repository | SAMtools.FastaIndex Indexes a reference sequence in FASTA format
Version: 2 |
Preprocess & Utilities | Module Repository | ScatterBlastSubtraction For the PathSeq pipeline, scatter a BWASubtraction job for each input fq1 file
Version: 8 |
pipeline | Module Repository | Scripture Segmentation-based transcript reconstruction algorithm
Version: 1 |
RNA-seq | Module Repository | ScripturePipeline Segmentation-based transcript reconstruction using single- or paired-end reads
Version: 3 |
pipeline | Module Repository | ScripturePrealigned Segmentation-based transcript reconstruction using pre-aligned reads
Version: 2 |
pipeline | Module Repository | SegmentationCount Counts the number of segments in a SEG file.
Version: 1 |
SNP Analysis | Module Repository | SelectFeaturesColumns Takes a 'column slice' from a .res, .gct, .snp, .cn, .loh, .odf, or .cls file.
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).
Version: 4 |
Gene List Selection | Module Repository | SelectFileMatrix A helper module which selects a matrix out of a delimited text file.
Version: 1 |
Preprocess & Utilities | Module Repository | SetFCSKeywords Sets keyword/value(s) in a Flow Cytometry Standard (FCS) file.
Version: 2 |
Flow Cytometry | Module Repository | SNPFileCreator Process Affymetrix SNP probe-level data into an expression value
Version: 1 |
SNP Analysis | Module Repository | SNPFileSorter Sorts a .snp file by Chromosome and location
Version: 1 |
SNP Analysis | Module Repository | SNPMultipleSampleAnalysis Determine Regions of Concordant Copy Number Aberrations
Version: |
SNP Analysis | Module Repository | SnpViewer Displays a heat map of snp data
Version: 3 |
Visualizer | Module Repository | SOMClustering Self-Organizing Maps algorithm
Version: 2 |
Clustering | Module Repository | SOMClusterViewer Visualize clusters created with the SOM algorithm
Version: 5 |
Visualizer | Module Repository | SortSam Sorts a SAM or BAM file in a specified order
Version: 3 |
Preprocess & Utilities | Module Repository | SparseHierarchicalClustering Cluster the samples in a data matrix using an adaptively-chosen subset of the features.
Version: 1 |
Clustering | Module Repository | SplitColumns Creates a separate file for each column specified from the input file
Version: 1 |
Preprocess & Utilities | Module Repository | SplitDatasetTrainTest Splits a dataset (and cls file) into a number of train and test subsets
Version: 4 |
Preprocess & Utilities | Module Repository | SraToFastQ Converts data in SRA format to FastQ using the SRAToolkit version 2.3.5-2.
Version: 1 |
RNA-seq | Module Repository | ssGSEAProjection Performs single sample GSEA Projection
Version: 9.1.2 |
Projection | Module Repository | StrandSpecRNAseqEval Evaluates strand-specific yeast (S. cerevisiae) RNA-seq libraries
Version: 1 |
RNA-seq | Module Repository | SubMap Maps subclasses between two data sets
Version: 3 |
Clustering | Module Repository | SubMapBrowser Surveys all possible subclass mappings
Version: 2 |
Clustering | Module Repository | SurvivalCurve Draws a survival curve based on a cls file
Version: 2 |
Survival Analysis | Module Repository | SurvivalDifference Tests for survival difference based on cls file
Version: 1 |
Survival Analysis | Module Repository | SVM Classify samples using SVM
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.
Version: 5 |
Data Format Conversion | Module Repository | TmapToGct Converts a TMAP file to GCT format
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.
Version: 8.11 |
RNA-seq | Module Repository | TransposeDataset Transpose a Dataset - .res .gct, .odf
Version: 3 |
Preprocess & Utilities | Module Repository | Trimmomatic Provides a variety of options for trimming Illumina FASTQ files of adapter sequences and low-quality reads.
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.
Version: 3 |
Data Format Conversion | Module Repository | UniquifyLabels Makes row and column labels unique
Version: 1 |
Preprocess & Utilities | Module Repository | VennDiagram Displays a Venn diagram
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"
Version: 0.9 |
Preprocess & Utilities | Module Repository | WeightedVoting Weighted Voting classification
Version: 3 |
Prediction | Module Repository | WeightedVotingXValidation Weighted Voting classification with Leave-One-Out Cross-Validation
Version: 3 |
Prediction | Module Repository | XChromosomeCorrect Corrects X Chromosome SNP's for male samples.
Version: 3 |
SNP Analysis | Module Repository |
|---|