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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 | Birdseed SNP genotyping algorithm that runs on the Affymetrix 500K, SNP5.0, and SNP6.0 platforms
Version: 1 |
SNP Analysis | * Public Server Only | BirdseedCallRate Computes the call rate of the Birdseed algorithm.
Version: 1 |
SNP Analysis | * Public Server Only | BirdseedDataPreparation Creates a set of BSNP files from a SNP file
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).
Version: 2 |
SNP Analysis | * Public Server Only | CopyNumberInference Infers copy number from probe intensity values
Version: 1 |
SNP Analysis | * Public Server Only | CopyNumberNoise Measures noise, calculates QC metrics on copy number data.
Version: 1 |
SNP Analysis | * Public Server Only | GISTIC_2.0 Genomic Identification of Significant Targets in Cancer
Version: 5 |
SNP Analysis | * Public Server Only | InsertGenomicLocations Inserts genomic locations into the output file from RemoveGenomicLocations
Version: 1 |
SNP Analysis | * Public Server Only | ParallelCBS Runs CBS algorithm on multiple samples in parallel
Version: 1 |
SNP Analysis | * Public Server Only | RemoveCopyNumberOutliers Reads rows of a copynumber file and removes outliers on a sample-by-sample basis.
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.
Version: 1 |
SNP Analysis | * Public Server Only | TangentNormalization Applies tangent normalization to copy number data
Version: 1 |
SNP Analysis | * Public Server Only | CNToXCN
Version: 1 |
SNP Analysis | Module Repository | CopyNumberDivideByNormals Determines the copy number of a target SNP
Version: 3 |
SNP Analysis | Module Repository | CopyNumberNoise Measures noise, calculates QC metrics on copynumber data.
Version: 1 |
SNP Analysis | Module Repository | GISTIC_2.0 Genomic Identification of Significant Targets in Cancer (version 2.0.23)
Version: 6.15.28 |
SNP Analysis | Module Repository | GLAD Gain and Loss Analysis of DNA
Version: 2 |
SNP Analysis | Module Repository | LOHPaired Computes LOH for paired samples
Version: 3 |
SNP Analysis | Module Repository | SegmentationCount Counts the number of segments in a SEG file.
Version: 1 |
SNP Analysis | Module Repository | SNPFileCreator Process Affymetrix SNP probe-level data into an expression value
Version: 1 |
SNP Analysis | Module Repository | SNPFileSorter Sorts a .snp file by Chromosome and location
Version: 1 |
SNP Analysis | Module Repository | SNPMultipleSampleAnalysis Determine Regions of Concordant Copy Number Aberrations
Version: |
SNP Analysis | Module Repository | XChromosomeCorrect Corrects X Chromosome SNP's for male samples.
Version: 3 |
SNP Analysis | Module Repository |
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