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.

View by Category:

NameTypeAvailability
Birdseed
SNP genotyping algorithm that runs on the Affymetrix 500K, SNP5.0, and SNP6.0 platforms
Pdf  Version: 1
SNP Analysis * Public Server Only
BirdseedCallRate
Computes the call rate of the Birdseed algorithm.
Pdf  Version: 1
SNP Analysis * Public Server Only
BirdseedDataPreparation
Creates a set of BSNP files from a SNP file
Pdf  Version: 1
SNP Analysis * Public Server Only
CBS
Segments DNA copy number data into regions of estimated equal copy number using circular binary segmentation (CBS).
Pdf  Version: 2
SNP Analysis * Public Server Only
CopyNumberInference
Infers copy number from probe intensity values
Pdf  Version: 1
SNP Analysis * Public Server Only
CopyNumberNoise
Measures noise, calculates QC metrics on copy number data.
Pdf  Version: 1
SNP Analysis * Public Server Only
GISTIC_2.0
Genomic Identification of Significant Targets in Cancer
Pdf  Version: 5
SNP Analysis * Public Server Only
InsertGenomicLocations
Inserts genomic locations into the output file from RemoveGenomicLocations
Pdf  Version: 1
SNP Analysis * Public Server Only
ParallelCBS
Runs CBS algorithm on multiple samples in parallel
Pdf  Version: 1
SNP Analysis * Public Server Only
RemoveCopyNumberOutliers
Reads rows of a copynumber file and removes outliers on a sample-by-sample basis.
Pdf  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.
Pdf  Version: 1
SNP Analysis * Public Server Only
TangentNormalization
Applies tangent normalization to copy number data
Pdf  Version: 1
SNP Analysis * Public Server Only
ABSOLUTE.review
Extracts the absolute copy number per cancer cell from a mixed DNA population. Use this module for the Review and Extract step in the workflow (after ABSOLUTE).
Html  Version: 1
SNP Analysis Module Repository
ABSOLUTE.summarize
Summarizes the results from multiple ABSOLUTE runs so that an analyst can manually review the solutions.
Html  Version: 1
SNP Analysis Module Repository
ABSOLUTE
Extracts absolute copy numbers per cancer cell from a mixed DNA population. Use this module for the per-sample processing step in the workflow (usually after HAPSEG).
Html  Version: 1
SNP Analysis Module Repository
CBS
Segments DNA copy number data into regions of estimated equal copy number using circular binary segmentation (CBS).
Html  Version: 3
SNP Analysis Module Repository
CNToXCN

Pdf  Version: 1
SNP Analysis Module Repository
CopyNumberDivideByNormals
Determines the copy number of a target SNP
Pdf  Version: 3
SNP Analysis Module Repository
CopyNumberNoise
Measures noise, calculates QC metrics on copynumber data.
Pdf  Version: 1
SNP Analysis Module Repository
GISTIC_2.0
Genomic Identification of Significant Targets in Cancer (version 2.0.23)
Html  Version: 6.14
SNP Analysis Module Repository
GLAD
Gain and Loss Analysis of DNA
Pdf  Version: 2
SNP Analysis Module Repository
HAPSEG
A probabilistic method to interpret bi-allelic marker data in cancer samples.
Html  Version: 1
SNP Analysis Module Repository
LOHPaired
Computes LOH for paired samples
Pdf  Version: 3
SNP Analysis Module Repository
SegmentationCount
Counts the number of segments in a SEG file.
Pdf  Version: 1
SNP Analysis Module Repository
SNPFileCreator
Process Affymetrix SNP probe-level data into an expression value
Pdf  Version: 1
SNP Analysis Module Repository
SNPFileSorter
Sorts a .snp file by Chromosome and location
Pdf  Version: 1
SNP Analysis Module Repository
SNPMultipleSampleAnalysis
Determine Regions of Concordant Copy Number Aberrations
Pdf  Version:
SNP Analysis Module Repository
XChromosomeCorrect
Corrects X Chromosome SNP's for male samples.
Pdf  Version: 3
SNP Analysis Module Repository