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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 | 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 Creates a GCT file from a set of CEL files from Affymetrix ST arrays. 
Version: 2 |
preprocess & utilities | Module Repository | Amaretto Discovery of driver genes using epigenomic, genomic and transcriptomic data using module networks with penalized regression.
Version: 2 |
Single-Cell | Module Repository | Amplicon.Architect A multithread-enabled quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. PrepareAA supports hg19 (or GRCh37), hg38 as well as mouse genome mm10 (or GRCm38). PrepareAA can also be invoked to start at intermediate stages of the data preparation process.\n\nAll credits go to\: https\://github.com/jluebeck/PrepareAA \n 
Version: 7 |
Module Repository | AmpliconSuite A multithread-enabled quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. PrepareAA supports hg19 (or GRCh37), hg38 as well as mouse genome mm10 (or GRCm38). PrepareAA can also be invoked to start at intermediate stages of the data preparation process.\n<br>\nAll credits go to\: https\://github.com/jluebeck/PrepareAA \n<br>\nView licenses here\: <a href\
Version: 40 |
ecdna | Module Repository | AmpliconSuiteAggregator Aggregates individual AmpliconSuite runs. Takes in zip files (or .tar.gz) and aggregates the results. Results can directly be used to load onto AmpliconRepository.
Version: 11 |
ecdna | 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 | BWA.aln 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: 2 |
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 | CellFie CellFie\: Cellular Functions InferencE - An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks. Please refer to the documentation for details about the procedure.
Version: 5 |
metabolomics | 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: 4.1 |
javascript | Module Repository | CNToXCN
Version: 1 |
SNP Analysis | Module Repository | CoGAPS Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.
Version: 1 |
Tutorial | Module Repository | CollapseDataset Collapses expression values from multiple input ids that map to a single target gene to a single value on a per-sample basis
Version: 2.1.5 |
Preprocess & Utilities | Module Repository | ComBat-Seq ComBat-Seq module. A Batch effect adjustment tool for bulk RNA-seq count data. Improvement upon ComBat, and uses a negative binomial regression to model batch effects. ComBat-seq takes untransformed, raw count matrix as input. Provides adjusted data which preserves the integer nature of counts, so that the adjusted data are compatible with the assumptions of state-of-the-art differential expression software (e.g. edgeR, DESeq2, which request untransformed count data)\nOriginal Documentation\: https\://github.com/zhangyuqing/ComBat-seq \nCredits go to Zhang et al, https\://doi.org/10.1093/nargab/lqaa078
Version: 4 |
Module Repository | ComBat Batch Correction - Not intended for use with single-cell RNA-seq data.
Version: 3.6 |
batch correction | Module Repository | ComBat_Seq ComBat_Seq module. A Batch effect adjustment tool for bulk RNA-seq count data. Improvement upon ComBat, and uses a negative binomial regression to model batch effects. ComBat-seq takes untransformed, raw count matrix as input. Provides adjusted data which preserves the integer nature of counts, so that the adjusted data are compatible with the assumptions of state-of-the-art differential expression software (e.g. edgeR, DESeq2, which request untransformed count data)\nOriginal Documentation\: https\://github.com/zhangyuqing/ComBat-seq \nCredits go to Zhang et al, https\://doi.org/10.1093/nargab/lqaa078
Version: 6.1 |
batch correction | Module Repository | ComparativeMarkerSelection Identify differentially expressed genes that can discriminate between distinct classes of samples.
Version: 11 |
gene list selection | Module Repository | ComparativeMarkerSelectionViewer Views the results from ComparativeMarkerSelection
Version: 9.1 |
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 | Conos.Cluster GenePattern Module which implements the clustering and embedding steps of Conos
Version: 3 |
clustering | Module Repository | Conos.Preprocess GenePattern Module which implements the preprocessing and PCA steps of Conos
Version: 3 |
clustering | Module Repository | Conos.VisualizeGeneExpression This is a minimalistic implementation of visualization options for Conos. This module is intended to be used after <a href\
Version: 8 |
single-cell | 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: 1.4.15 |
Pathway Analysis | Module Repository | Convert.Alevin Read alevin output files and convert them to anndata (.h5ad) or loom (.loom) format for downstream analysis. Designed to convert Alevin Velocity quantification into a compatible format for scVelo.
Version: 1 |
singlecell | 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: 3 |
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 | 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 | DAPPLE DAPPLE (Disease Association Protein-Protein Link Evaluator) looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature.
Version: 0.19 |
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: 3 |
differential expression | Module Repository | DifferentialExpressionViewer Views differential expression results such as from the ComparativeMarkerSelection module. Formerly known as ComparativeMarkerSelectionViewer.
Version: 10 |
javascript | 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 | ESPPredictor Determine which tryptic peptides will generate the highest signal in ESI-MS
Version: 4 |
proteomics | Module Repository | ExampleModule This is an example GenePattern module written in Python 3. It can be used as a template for future modules. It reads a file and potentially adds a line of text
Version: 3 |
administration | 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: 6 |
Preprocess & Utilities | Module Repository | GISTIC_2.0 Genomic Identification of Significant Targets in Cancer (version 2.0.23)
Version: 6.15.28 |
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: 3 |
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: 20.3.6 |
Pathway Analysis | Module Repository | GSEALeadingEdgeViewer Leading Edge Viewer for GSEA results
Version: 6 |
Visualizer | Module Repository | GSEAPreranked Runs the gene set enrichment analysis against a user-supplied ranked list of genes.
Version: 7.3.4 |
Pathway Analysis | Module Repository | Harmony Harmony is a batch correction tool. Upon use, this module will produce three scatterplots. One plot will show the data pre-Harmony, and can be found in the 'BeforeHarmonyPlot.png' file. In this plot, the x and y axes represent the 1st and 2nd principal components from PCA dimensional reduction (unless specified otherwise by the user). Another plot will show the data post-Harmony, and can be found in the 'AfterHarmonyPlot.png' file. In this plot, the x and y axes the same dimensions used in the pre-Harmony plot are shown, but adjusted by Harmony. Lastly, the third plot shows the pre-Harmony and post-Harmony plots side by side for comparison.
Version: 6 |
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: 13.11 |
javascript | Module Repository | HierarchicalClustering Perform hierarchical clustering on samples (columns) or/and genes (rows).
Version: 7.14 |
Clustering | 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: 11.4 |
javascript | Module Repository | HISAT2.aligner 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: 3 |
rna-seq | Module Repository | HISAT2.indexer Indexes one or more Fasta files for use in the HISAT2.aligner.
Version: 1.9 |
RNA-Seq | 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 | HTSeq.Count Takes alignment files in SAM/BAM format and a feature file in GTF/GFF format (usually with exon annotation), name sorts the alignment file and calculates for each sample the number of reads mapping to each feature. (HTSeq.count v0.11.2)
Version: 4 |
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: 2.5 |
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.Indexer Builds an index from a FASTA formatted file of target sequences for use with Kallisto.
Version: 2 |
Module Repository | Kallisto.Quant Runs Kallisto to perform pseudoalignment (using a human or mouse transcriptome index) and gene-level aggregation
Version: 4 |
rna-seq | Module Repository | Kallisto Runs Kallisto to perform pseudoalignment (using a human or mouse transcriptome index) and gene-level aggregation
Version: 3 |
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.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 | 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: 1 |
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: 4 |
Methylation | 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 | NearestTemplatePrediction Nearest neighbor prediction based on a list of marker genes
Version: 6 |
Prediction | Module Repository | NMF Non-negative Matrix Factorization
Version: 2.1 |
Dimension Reduction | Module Repository | NMFConsensus Non-negative Matrix Factorization (NMF) Consensus Clustering
Version: 5 |
Clustering | Module Repository | OpenCRAVAT <img src\
Version: 1 |
variant annotation | Module Repository | OutSplice.plotJunctions Using the result file from OutSplice, OutSplice.plotJunctions creates bar and waterfall plots of junction expression in both the tumor and normal samples.
Version: 3 |
beta | Module Repository | OutSplice OutSplice is a package that compares alternative splicing events between tumor and normal samples. This package is specifically designed for analyzing the gene and junction information from RNA sequencing data provided by the user, or from the TCGA. This package generates a matrix of splicing outliers, which are junctions that are either significantly over or under-expressed compared to a control sample. OutSplice further designates observed outliers as skipping, insertion, or deletion events. Overall, OutSplice is novel in that it determines differential splicing burdens between tumors and normal samples and characterizes the nature of splicing outliers.
Version: 3 |
beta | Module Repository | PCA Principal Component Analysis (adapted from MeV, <a href
Version: 4.1 |
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, indexes BAM files, and interconverts SAM and BAM files.
Version: 4 |
Preprocess & Utilities | * Public Server Only | Picard.SortSam Sorts a SAM or BAM file in a specified order
Version: 4 |
Preprocess & Utilities | Module Repository | PlotPeaks Plot peaks
Version: 2 |
Proteomics | 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 | PreprocessVelocityTranscriptome Extract transcript and intron sequences from the genome sequence using the eisaR package in order to quantify both intronic (unprocessed) and exonic (processed) RNA abundances in each cell with alevin.<br>A necessary preprocessing step to enable RNA velocity analysis.
Version: 1 |
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 | PyCoGAPS Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis. This package, PyCoGAPS, presents a unified Python interface, with a parallel, efficient underlying implementation.
Version: 4 |
beta | 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 | RandomForest.GPU GPU-backed implementation to perform random forest classification (cross-validation or test-train prediction), outputting prediction results (and feature importance for test-train mode with datasets). It uses the CuPy implementation which might be faster compared to regular RandomForest.
Version: 0 |
prediction | Module Repository | RandomForest Performs random forest classification on data and class files (cross-validation or test-train prediction), outputting a prediction results file.
Version: 4 |
prediction | 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 | Salmon.Alevin.Quant Quantification and analysis of 3' tagged-end single-cell sequencing data using Salmon's Alevin (v1.5.2) function.<br>\n\nSee\: <a href\
Version: 0.6 |
rna-seq | Module Repository | Salmon.Indexer Salmon (version 1.6.0) transcriptome indexer.<br>\n\nSee\: <a href\
Version: 0.5 |
rna-seq | Module Repository | Salmon.Quant Perform transcript-level quantification of RNA-seq data using Salmon (version 1.6.0).<br>\n\nSee\: <a href\
Version: 0.9 |
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 | ScanpyQC Create Scanpy Quality Control Plots to enable unblinded dataset filtering with ScanpyUtilities
Version: 2 |
singlecell | Module Repository | ScanpyUtilities Scanpy preprocessing of an h5 single cell RNASeq dataset
Version: 1 |
Single-Cell | 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 | scVelo Module for performing basic velocity analysis using the scVelo protocol on ScanpyUtilities processed datasets
Version: 2 |
single-cell | 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 | Seurat.BatchCorrection Batch Correction for Seurat Objects
Version: 3 |
singlecell | Module Repository | Seurat.Clustering Companion module for the <a href\
Version: 1 |
SingleCell | Module Repository | Seurat.IntegrateData Batch Correction for Seurat Objects
Version: 4.1 |
dimension reduction | Module Repository | Seurat.Preprocessing Seurat preprocessing
Version: 4 |
preprocess & utilities | Module Repository | Seurat.QC Seurat quality control (First step in the Seurat Suite), using Seurat version 4.0.3.
Version: 4 |
preprocess & utilities | Module Repository | Seurat.VisualizeMarkerExpression Visualize Marker Expression as violin plots and on a UMap. To be used after Seurat.Clustering
Version: 2 |
single-cell | 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 | spatialGE.Preprocessing The package spatialGE provides a collection of tools for the visualization of gene expression from spatially-resolved transcriptomic experiments. The data input methods have been designed so that any data can be analyzed as long as it contains gene expression counts per region of interest (ROI), spot, or cell, and the spatial coordinates of those ROIs, spots, or cells, as it is generated in platforms such as GeoMx, Visium, and CosMx-SMI. The spatialge.Preprocessing module performs initial data ingestion, filtering, transform and pseudo-bulk operations to prepare data for further processing. Order of operations are\: ingestion, filter, pseudobulk, transform.
Version: 2 |
administration | Module Repository | spatialGE.STenrich Detect genes showing spatial expression patterns (e.g., hotspots). Tests if spots/cells with high average expression of a gene set shows evidence of spatial aggregation.
Version: 1 |
spatial transcriptomics | 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 | ssGSEA.ROC Generate ROC curves and calculate the AUC from ssGSEA results and a binary phenotype classification.
Version: 1 |
beta | Module Repository | ssGSEA Performs single sample GSEA. NOTE\: with the release of v10.0.1, this module was renamed from "ssGSEAProjection" to just "ssGSEA"
Version: 10.0.12 |
Pathway Analysis | Module Repository | ssGSEAProjection Performs single sample GSEA Projection
Version: 9.1.2 |
Projection | Module Repository | STAR.aligner STAR (Spliced Transcripts Alignment to a Reference) 2.7.10b is a fast RNA-seq reads to genome mapper. It differs from other mappers as TopHat in that it gains speed at the expense of consuming more RAM and that it incorporates transcriptome annotation at the indexing build stage rather than at the analysis stage. It can optionally detect non-canonical splices and chimeric transcripts.
Version: 2 |
RNA-seq | Module Repository | STAR.indexer The STAR indexer (version 2.7.10b) makes from a series of fastA files containing a genome an index for use with the STAR spliced read to genome aligner. It can optionally (but highly recommended \!) incorporate information about known intron-exon junctions.
Version: 1 |
RNA-seq | 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: 4 |
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 | TCGA.SampleSelection Retrieve TCGA data from Broad FireBrowse and perform sample selection on the basis of expression levels for specific genes of interest for analysis using GSEA tools.
Version: 3 |
preprocess & utilities | 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: 6 |
Data Format Conversion | Module Repository | TmapToGct Converts a TMAP file to GCT format
Version: 1 |
Data Format Conversion | 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: 2 |
RNA-seq | Module Repository | tximport.DESeq2 Imports RNA-seq quantifications from frequently used pipelines using the tximport package and outputs a DESeq2 "normalized counts" file in .GCT format suitable for use with GSEA, and/or a TPM .GCT suitable for ssGSEA.<br>\nIf a Sample Info file is provided containing assignments of samples to phenotypes, gene level differential expression will be calculated using DESeq2 for the two phenotypes.
Version: 5 |
differential expression | 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: 1 |
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 |
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