GenePattern Modules

Modules in the repository can be installed on a local GenePattern server. Most of these modules are also installed on the public GenePattern server.

View by Category:

NameTypeAvailability
Arff2Gct
Convert an .arff file into a GenePattern .gct / .cls file pair
Pdf  Version: 0.4
Preprocess & Utilities * Public Server Only
ComBat
Performs batch correction on a dataset containing multiple batches
Html  Version: 3
Preprocess & Utilities * Public Server Only
CombineOdf
Combine two prediction results files into a single, weighted, multi-label prediction results file
Pdf  Version: 0.4
Preprocess & Utilities * Public Server Only
ExpressionFileCreator
Creates a RES or GCT file from a set of Affymetrix CEL files
Pdf  Version: 11
Preprocess & Utilities * Public Server Only
Gct2Arff
Convert a GenePattern .gct / .cls file pair into an .arff file
Pdf  Version: 0.3
Preprocess & Utilities * Public Server Only
IlluminaConcatenator
Concatenate normalized Illumina probe sets into a single GCT file
Pdf  Version: 1
Preprocess & Utilities * Public Server Only
IlluminaNormalizer
Normalize zipped Illumina scans
Pdf  Version: 1
Preprocess & Utilities * Public Server Only
IlluminaScanExtractor
Extract intensity values from Illumina scans
Pdf  Version: 1
Preprocess & Utilities * Public Server Only
Picard.SortSam
Sorts a SAM or BAM file in a specified order, indexes BAM files, and interconverts SAM and BAM files.
Html  Version: 4
Preprocess & Utilities * Public Server Only
ProteinDatasetCreation
Extract features from protein .FASTA files for use with standard prediction algorithms
Pdf  Version: 0.4
Preprocess & Utilities * Public Server Only
AddOrReplaceReadGroups
Replaces all read groups in the input file with a new read group and assigns all reads to this read group in the output
Pdf  Version: 1
Preprocess & Utilities Module Repository
CollapseDataset
Collapses all probe set values for a gene into a single vector of values
Pdf  Version: 1
Preprocess & Utilities Module Repository
ComBat
Batch Correction
Pdf  Version: 2
Preprocess & Utilities Module Repository
ConcatenateFilelist
Concatenate all of the items in the input filelist into a single large file.
Pdf  Version: 1
Preprocess & Utilities Module Repository
ConvertLineEndings
Converts line endings to the host operating system's format.
Pdf  Version: 1
Preprocess & Utilities Module Repository
ConvertToMAGEML
Converts a gct, res, or odf dataset file to a MAGE-ML file
Pdf  Version: 2
Preprocess & Utilities Module Repository
ConvertToMAGETAB
A module to export data from GenePattern in MAGE-TAB format
Pdf  Version: 2
Preprocess & Utilities Module Repository
CreateSymlinks
Creates symlinks to the input files in the job results directory. This is intended to be a helper module for creating scatter-gather pipelines. Note that this module is not supported on Windows
Html  Version: 1
Preprocess & Utilities Module Repository
DownloadURL
Downloads a file from a URL
Pdf  Version: 1
Preprocess & Utilities Module Repository
ExpressionFileCreator
Creates a RES or GCT file from a set of Affymetrix CEL files
Pdf  Version: 7
Preprocess & Utilities Module Repository
ExtractColumnNames
Lists the sample descriptors from a .res file.
Pdf  Version: 2
Preprocess & Utilities Module Repository
ExtractRowNames
Extracts the row names from a .res, .gct, or .odf file.
Pdf  Version: 3
Preprocess & Utilities Module Repository
FileSplitter
Splits a file into equal-sized chunks, given the number of lines per output file
Pdf  Version: 2
Preprocess & Utilities Module Repository
FilterFilelist
a helper module which generates a filtered filelist from the input filelist and some filter parameters.
Pdf  Version: 1
Preprocess & Utilities Module Repository
GenePatternDocumentExtractor
Extracts GenePattern pipelines and other embedded GenePattern data from Word 2007 documents created with the Microsoft Word Add-In for the GenePattern Reproducible Research Document.
Pdf  Version: 1
Preprocess & Utilities Module Repository
GEOImporter
Imports data from the Gene Expression Omnibus (GEO)
Pdf  Version: 5
Preprocess & Utilities Module Repository
Hu68kHu35kAtoU95
Converts a list of Affymetrix Hu6800/Hu35KsubA probes to the corresponding Affymetrix U95Av2 probes.
Pdf  Version: 1
Preprocess & Utilities Module Repository
IlluminaExpressionFileCreator
Creates a GCT file from a zip of Illumina IDAT files and an Illumina manifest file
Pdf  Version: 2
Preprocess & Utilities Module Repository
MapChipFeaturesGeneral
Change (map) the features (genes) of a dataset
Pdf  Version: 3
Preprocess & Utilities Module Repository
MergeColumns
Merge datasets by column.
Pdf  Version: 1
Preprocess & Utilities Module Repository
MergeRows
Merge datasets by row.
Pdf  Version: 1
Preprocess & Utilities Module Repository
MultiplotPreprocess
Creates derived data from an expression dataset for use in the Multiplot Visualizer module
Pdf  Version: 1
Preprocess & Utilities Module Repository
Picard.AddOrReplaceReadGroups
Replaces all read groups in the input file with a new read group and assigns all reads to this read group in the output
Pdf  Version: 3
Preprocess & Utilities Module Repository
Picard.CreateSequenceDictionary
Reads FASTA or FASTA.GZ files containing reference sequences, and writes them as a SAM file containing a sequence dictionary
Pdf  Version: 1
Preprocess & Utilities Module Repository
Picard.MarkDuplicates
Examines aligned records in the supplied SAM or BAM file to locate duplicate reads.
Pdf  Version: 2
Preprocess & Utilities Module Repository
Picard.ReorderSam
Reorders a SAM file or a BAM file to match contig ordering in a provided reference file
Pdf  Version: 1
Preprocess & Utilities Module Repository
Picard.SortSam
Sorts a SAM or BAM file in a specified order
Pdf  Version: 4
Preprocess & Utilities Module Repository
PreprocessDataset
Performs several preprocessing steps on a res, gct, or odf input file
Html  Version: 5
Preprocess & Utilities Module Repository
RenameFile
Creates a result file with the contents of the input but with a new name. Where possible, this is done without copying the file but instead by simply making a link. While it is possible to run this with a submitted file, the common use will be to change the name of a result file or a previously uploaded file. Note that the original file will still be present in its original location.
Html  Version: 1
Preprocess & Utilities Module Repository
ReorderByClass
Reorder the samples in an expression dataset and class file by class
Pdf  Version: 3
Preprocess & Utilities Module Repository
SAMtools.FastaIndex
Indexes a reference sequence in FASTA format
Html  Version: 2
Preprocess & Utilities Module Repository
SelectFileMatrix
A helper module which selects a matrix out of a delimited text file.
Pdf  Version: 1
Preprocess & Utilities Module Repository
SortSam
Sorts a SAM or BAM file in a specified order
Pdf  Version: 3
Preprocess & Utilities Module Repository
SplitColumns
Creates a separate file for each column specified from the input file
Pdf  Version: 1
Preprocess & Utilities Module Repository
SplitDatasetTrainTest
Splits a dataset (and cls file) into a number of train and test subsets
Pdf  Version: 4
Preprocess & Utilities Module Repository
TransposeDataset
Transpose a Dataset - .res .gct, .odf
Pdf  Version: 3
Preprocess & Utilities Module Repository
UniquifyLabels
Makes row and column labels unique
Pdf  Version: 1
Preprocess & Utilities Module Repository