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 |
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 |
GISTICPreprocess
Prepare SNP files for GISTIC
Version: 2 |
SNP Analysis |
* 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 |
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 |
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 |
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: 5 |
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 |
Bowtie.aligner
An ultrafast, memory-efficient short read aligner
Version: 3 |
RNA-seq |
Module Repository |
Bowtie.indexer
Builds a Bowtie index from a set of DNA sequences
Version: 1 |
RNA-seq |
Module Repository |
BWA.aln
A fast light-weighted tool that aligns long reads to a sequence database
Version: 1 |
RNA-seq |
Module Repository |
BWA.bwasw
A fast light-weight tool that aligns long sequences (>200 bp) to a sequence database
Version: 1 |
RNA-seq |
Module Repository |
BWA.indexer
Creates a BWT index from a sequence FASTA file
Version: 1 |
RNA-seq |
Module Repository |
CaArray2.1.0Importer
Imports data files from CaArray 2.1.0 and zips them up.
Version: 38 |
caBIG |
Module Repository |
CaArray2.3.0Importer
Imports data files from CaArray 2.3.X and zips them up.
Version: 4 |
caBIG |
Module Repository |
CaArray2ImportViewer
Imports data files from CaArray 2.4.1 and creates gct or cls files
Version: 1 |
Visualizer |
Module Repository |
caArrayImportViewer
A visualizer to import data from caArray into GenePattern via the mage-om api
Version: 1 |
Visualizer |
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: 1 |
SNP Analysis |
Module Repository |
ClassNeighbors
Select genes that most closely resemble a profile
Version: 1 |
Gene List Selection |
Module Repository |
ClsFileCreator
A tool to create a class label (CLS) file.
Version: 2 |
Visualizer |
Module Repository |
CNToXCN
Version: 1 |
SNP Analysis |
Module Repository |
CollapseDataset
Collapses all probe set values for a gene into a single vector of values
Version: 1 |
Preprocess & Utilities |
Module Repository |
ComBat
Batch Correction
Version: 2 |
Preprocess & Utilities |
Module Repository |
ComparativeMarkerSelection
Computes significance values for features using several metrics, including FDR(BH), Q-Value, maxT, FWER, Feature-Specific P-Value, and Bonferroni.
Version: 9 |
Gene List Selection |
Module Repository |
ComparativeMarkerSelectionViewer
Views the results from ComparativeMarkerSelection
Version: 4 |
Visualizer |
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 |
Clustering |
Module Repository |
ConvertLineEndings
Converts line endings to the host operating system's format.
Version: 1 |
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 |
CopyNumberDivideByNormals
Determines the copy number of a target SNP
Version: 3 |
SNP Analysis |
Module Repository |
CoxRegression
Cox regression using clinical data and .cls file
Version: 1 |
Survival Analysis |
Module Repository |
CsvToFcs
Converts a Comma separated values (CSV) file to a Flow Cytometry Standard (FCS) file.
Version: 2 |
Data Format Conversion |
Module Repository |
Cufflinks.cuffcompare
Analyzes the transcribed fragments in an assembly
Version: 4 |
RNA-seq |
Module Repository |
Cufflinks.cuffdiff
Cufflinks 2.0.2 - Finds significant changes in transcript expression, splicing, and promoter use
Version: 4 |
RNA-seq |
Module Repository |
Cufflinks.cuffmerge
Cufflinks 2.0.2\: Cuffmerge - Merge several Cufflinks assemblies
Version: 1 |
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: 4 |
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 |
DownloadURL
Downloads a file from a URL
Version: 1 |
Preprocess & Utilities |
Module Repository |
ExpressionFileCreator
Creates a RES or GCT file from a set of Affymetrix CEL files
Version: 7 |
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 |
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 |
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 |
GENE_E
Launches GENE-E with input file(s)
Version: 1 |
GENE-E |
Module Repository |
GeneCruiser
Retrieve gene annotations for Affy probe ids from GeneCruiser
Version: 7 |
Annotation |
Module Repository |
GeneListSignificanceViewer
Views the results of marker analysis
Version: 4 |
Visualizer |
Module Repository |
GeneNeighbors
Select genes that most closely resemble a continuous profile (e.g., another gene)
Version: 4 |
Gene List Selection |
Module Repository |
GenePatternDocumentExtractor
Extracts GenePattern pipelines and other embedded GenePattern data from Word 2007 documents created with the Microsoft Word Add-In for the GenePattern Reproducible Research Document.
Version: 1 |
Preprocess & Utilities |
Module Repository |
GEOImporter
Imports data from the Gene Expression Omnibus (GEO)
Version: 5 |
Preprocess & Utilities |
Module Repository |
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
Version: 13 |
Gene List Selection |
Module Repository |
GSEALeadingEdgeViewer
Leading Edge Viewer for GSEA results
Version: 2 |
Visualizer |
Module Repository |
HeatMapImage
Creates a heat map from a dataset
Version: 6 |
Image Creators |
Module Repository |
HeatMapViewer
Displays a heat map
Version: 10 |
Visualizer |
Module Repository |
HierarchicalClustering.MATLAB
Hierarchical Clustering
Version: 0 |
Clustering |
Module Repository |
HierarchicalClustering
Hierarchical Clustering
Version: 5 |
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: 3 |
Image Creators |
Module Repository |
HierarchicalClusteringViewer
Views results of hierarchical clustering.
Version: 10 |
Visualizer |
Module Repository |
Hu68kHu35kAtoU95
Converts a list of Affymetrix Hu6800/Hu35KsubA probes to the corresponding Affymetrix U95Av2 probes.
Version: 1 |
Preprocess & Utilities |
Module Repository |
IGV
Launches IGV with input file(s)
Version: 4 |
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 |
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 |
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 |
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: 1 |
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 |
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 |
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: 1 |
Visualizer |
Module Repository |
MultiplotExtractor
Creates customizable plots of expression data-derived data.
Version: 1 |
Visualizer |
Module Repository |
MultiplotPreprocess
Creates derived data from an expression dataset for use in the Multiplot Visualizer module
Version: 1 |
Preprocess & Utilities |
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: 1 |
Prediction |
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 |
PCA
Principal Component Analysis (adapted from MeV, http\://www.tm4.org/m)
Version: 4 |
Projection |
Module Repository |
PCAViewer
Principal Component Analysis Visualizer (adapted from MeV, http\://www.tigr.org/software/tm4/mev.html)
Version: 6 |
Visualizer |
Module Repository |
PclToGct
Convert Stanford preclustering file (.pcl) to .gct
Version: 1 |
Data Format Conversion |
Module Repository |
PeakMatch
Perform peak matching on LC-MS data
Version: 2 |
Proteomics |
Module Repository |
Peaks
Determine peaks in the spectrum using a series of digital filters.
Version: 2 |
Proteomics |
Module Repository |
Picard.AddOrReplaceReadGroups
Replaces all read groups in the input file with a new read group and assigns all reads to this read group in the output
Version: 3 |
Preprocess & Utilities |
Module Repository |
Picard.BamToSam
Converts a BAM file to a SAM file
Version: 2 |
Data Format Conversion |
Module Repository |
Picard.CreateSequenceDictionary
Reads FASTA or FASTA.GZ files containing reference sequences, and writes them as a SAM file containing a sequence dictionary
Version: 1 |
Preprocess & Utilities |
Module Repository |
Picard.FastqToSam
Extracts read sequences and qualities from the input fastq file and writes them into the output file in unaligned SAM or BAM format
Version: 2 |
Data Format Conversion |
Module Repository |
Picard.MarkDuplicates
Examines aligned records in the supplied SAM or BAM file to locate duplicate reads.
Version: 2 |
Preprocess & Utilities |
Module Repository |
Picard.ReorderSam
Reorders a SAM file or a BAM file to match contig ordering in a provided reference file
Version: 1 |
Preprocess & Utilities |
Module Repository |
Picard.SamToBam
Converts a SAM file to a BAM file
Version: 2 |
Data Format Conversion |
Module Repository |
Picard.SamToFastq
Convert SAM or BAM files to FASTQ format
Version: 2 |
Data Format Conversion |
Module Repository |
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 |
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: 4 |
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 |
RankNormalize
Normalize the rows in a data set by rank
Version: 1 |
Statistical Methods |
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 |
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: 1 |
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 |
SelectFeaturesColumns
Takes a 'column slice' from a .res, .gct, .snp, .cn, .loh, .odf, or .cls file.
Version: 4 |
Gene List Selection |
Module Repository |
SelectFeaturesRows
Generate a .res, .gct, .snp, .cn, .loh, or .odf file containing only specified features (i.e. rows).
Version: 4 |
Gene List Selection |
Module Repository |
SelectFileMatrix
A helper module which selects a matrix out of a delimited text file.
Version: 1 |
Preprocess & Utilities |
Module Repository |
SetFCSKeywords
Sets keyword/value(s) in a Flow Cytometry Standard (FCS) file.
Version: 2 |
Flow Cytometry |
Module Repository |
SNPFileCreator
Process Affymetrix SNP probe-level data into an expression value
Version: 1 |
SNP Analysis |
Module Repository |
SNPFileSorter
Sorts a .snp file by Chromosome and location
Version: 1 |
SNP Analysis |
Module Repository |
SNPMultipleSampleAnalysis
Determine Regions of Concordant Copy Number Aberrations
Version: |
SNP Analysis |
Module Repository |
SnpViewer
Displays a heat map of snp data
Version: 3 |
Visualizer |
Module Repository |
SOMClustering
Self-Organizing Maps algorithm
Version: 2 |
Clustering |
Module Repository |
SOMClusterViewer
Visualize clusters created with the SOM algorithm
Version: 5 |
Visualizer |
Module Repository |
SortSam
Sorts a SAM or BAM file in a specified order
Version: 3 |
Preprocess & Utilities |
Module Repository |
SparseHierarchicalClustering
Cluster the samples in a data matrix using an adaptively-chosen subset of the features.
Version: 1 |
Clustering |
Module Repository |
SplitColumns
Creates a separate file for each column specified from the input file
Version: 1 |
Preprocess & Utilities |
Module Repository |
SplitDatasetTrainTest
Splits a dataset (and cls file) into a number of train and test subsets
Version: 4 |
Preprocess & Utilities |
Module Repository |
ssGSEAProjection
Performs single sample GSEA Projection
Version: 3 |
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 |
TmapToGct
Converts a TMAP file to GCT format
Version: 1 |
Data Format Conversion |
Module Repository |
TopHat
TopHat 2.0.8b is a fast splice junction mapper. It aligns RNA-Seq reads and then analyzes the mapping results to identify splice junctions between exons.
Version: 6 |
RNA-seq |
Module Repository |
TransposeDataset
Transpose a Dataset - .res .gct, .odf
Version: 3 |
Preprocess & Utilities |
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 |
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 |
