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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 | 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 | CsvToFcs Converts a Comma separated values (CSV) file to a Flow Cytometry Standard (FCS) file.
Version: 2 |
Data Format Conversion | Module Repository | ExprToGct Converts an EXPR file to GCT format
Version: 2 |
Data Format Conversion | 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 | GctToPcl Convert .gct to .pcl
Version: 1 |
Data Format Conversion | Module Repository | PclToGct Convert Stanford preclustering file (.pcl) to .gct
Version: 1 |
Data Format Conversion | Module Repository | Picard.BamToSam Converts a BAM file to a SAM file
Version: 2 |
Data Format Conversion | 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.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 | 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 | 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 | 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 |
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