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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 | Arff2Gct Convert an .arff file into a GenePattern .gct / .cls file pair
Version: 0.4 |
Preprocess & Utilities | * 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 | ExpressionFileCreator Creates a RES or GCT file from a set of Affymetrix CEL files
Version: 11 |
Preprocess & Utilities | * 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 | 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 | ProteinDatasetCreation Extract features from protein .FASTA files for use with standard prediction algorithms
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
Version: 1 |
Preprocess & Utilities | 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 | ConcatenateFilelist Concatenate all of the items in the input filelist into a single large file.
Version: 1 |
Preprocess & Utilities | 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 | 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 | DownloadURL Downloads a file from a URL
Version: 1 |
Preprocess & Utilities | Module Repository | ExpressionFileCreator Creates a RES or GCT file from a set of Affymetrix CEL files. For IVT arrays only; use AffySTExpressionFileCreator for ST arrays.
Version: 12 |
Preprocess & Utilities | Module Repository | ExtractColumnNames Lists the sample descriptors from a .res file.
Version: 2 |
Preprocess & Utilities | Module Repository | ExtractRowNames Extracts the row names from a .res, .gct, or .odf file.
Version: 3 |
Preprocess & Utilities | 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 | 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 | Hu68kHu35kAtoU95 Converts a list of Affymetrix Hu6800/Hu35KsubA probes to the corresponding Affymetrix U95Av2 probes.
Version: 1 |
Preprocess & Utilities | 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 | 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 | 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 | MergeRows Merge datasets by row.
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
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
Version: 1 |
Preprocess & Utilities | 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.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 | 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 | 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 | SelectFileMatrix A helper module which selects a matrix out of a delimited text file.
Version: 1 |
Preprocess & Utilities | Module Repository | SortSam Sorts a SAM or BAM file in a specified order
Version: 3 |
Preprocess & Utilities | 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 | 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 | 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 |
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