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
Creates a GCT file from a set of CEL files from Affymetrix ST arrays.
Version: 2 |
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 |
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
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: 4 |
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 |
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: 2.0.1 |
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: 1.4.15 |
Pathway Analysis |
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 |
ESPPredictor
Determine which tryptic peptides will generate the highest signal in ESI-MS
Version: 4 |
proteomics |
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: 6.14 |
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: 20.2.3 |
Pathway Analysis |
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: 7.2.3 |
Pathway Analysis |
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 |
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: 3 |
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 |
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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 |
OpenCRAVAT
<img src\
Version: 1 |
variant annotation |
Module Repository |
ParallelCBS
Runs CBS algorithm on multiple samples in parallel
Version: 1 |
pipeline |
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
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 |
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 |
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.Preprocessing
Seurat preprocessing
Version: 1 |
preprocess & utilities |
Module Repository |
Seurat.QC
Seurat quality control (First step in the Seurat Suite), using Seurat version 3.2.0.
Version: 3 |
preprocess & utilities |
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 |
ssGSEA
Performs single sample GSEA. NOTE\: with the release of v10.0.1, this module was renamed from "ssGSEAProjection" to just "ssGSEA"
Version: 10.0.7 |
Pathway Analysis |
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: 6 |
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: 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 |