GenePattern Modules


Click the Html or Pdf icons to view a module's documentation.

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

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NameTypeAvailability
BamToSam
Converts a BAM file to a SAM file
Pdf  Version: 1
Data Format Conversion Module Repository
BedToGtf
Converts BED files to GFF or GTF format
Pdf  Version: 1
Data Format Conversion Module Repository
CsvToFcs
Converts a Comma separated values (CSV) file to a Flow Cytometry Standard (FCS) file.
Pdf  Version: 2
Data Format Conversion Module Repository
ExprToGct
Converts an EXPR file to GCT format
Pdf  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
Pdf  Version: 1
Data Format Conversion Module Repository
FcsToCsv
Converts a Flow Cytometry Standard (FCS) file to a Comma Separated Values (CSV) file.
Pdf  Version: 3
Data Format Conversion Module Repository
GctToPcl
Convert .gct to .pcl
Pdf  Version: 1
Data Format Conversion Module Repository
PclToGct
Convert Stanford preclustering file (.pcl) to .gct
Pdf  Version: 1
Data Format Conversion Module Repository
Picard.BamToSam
Converts a BAM file to a SAM file
Pdf  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
Pdf  Version: 2
Data Format Conversion Module Repository
Picard.SamToBam
Converts a SAM file to a BAM file
Pdf  Version: 2
Data Format Conversion Module Repository
Picard.SamToFastq
Convert SAM or BAM files to FASTQ format
Html  Version: 3
Data Format Conversion Module Repository
SamToBam
Converts a SAM file to a BAM file
Pdf  Version: 1
Data Format Conversion Module Repository
SamToFastq
Convert SAM or BAM files to FASTQ format
Pdf  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.
Html  Version: 5
Data Format Conversion Module Repository
TmapToGct
Converts a TMAP file to GCT format
Pdf  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.
Html  Version: 3
Data Format Conversion Module Repository