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PennCNV

A free software tool for copy number variation (CNV) detection from SNP genotyping arrays. PennCNV can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs from segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.

VegaMC

A package for fast downstream analysis of large array comparative genomic hybridization datasets. VegaMC enables fast and efficient detection of significant recurrent copy number alterations in very large datasets. It is integrated with the output of the common tools that convert allele signal intensities in log R ratio and B allele frequency. VegaMC also enables the detection of loss of heterozigosity and provides in output two web pages allowing a rapid and easy navigation of the aberrant genes. Synthetic data and real datasets are used for quantitative and qualitative evaluation purposes. By exploiting a multichannel segmentation algorithm, this package identifies the driver genes from LRR and BAF observations. It also enables an easy navigation of the results by html pages.

UPDtool

A computational tool for detection and classification of uniparental disomy (UPD) in trio SNP-microarray experiments. We were able to detect hetero- and isodisomies from maternal and paternal origin present in our positive controls. All UPD stretches were identified correctly, and breakpoints within a chromosome could be determined more precisely compared with microsatellite analysis. UPDtool is platform independent, light weight and flexible. Because of its simple input format, UPDtool may also be used with other high-throughput technologies (e.g., next-generation sequencing).

StrandScript

Converts all genotyping data generated from Illumina genotyping arrays to the reference forward strand. StrandScript works independently of the Illumina array version and is future proof for newer Illumina array designs. It can detect all problematic single nucleotide polymorphism (SNPs), including SNPs with wrong RS ID and SNPs with mismatched probe sequences in an Illumina genotyping array manifest file. The tool does not require the pre-processed conversion file for each array.

maPredictDSC

Implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. maPredictDSC facilitates the development of microarray-based prediction models. The package offers the possibility to automatically search among a large number of combinations of methods for the one that maximizes the cross-validated performance on the training data. An implementation of the ‘wisdom of crowds’ is offered by combining the predictions of the resulting models.

BASH / BeadArray Subversion of Harshlight

Adopts the concepts of Harshlight, but implements them in a manner that utilizes the unique characteristics of the Illumina technology. BASH requires knowledge of the direct neighbours of a bead, and the identities of other ‘nearby’ beads. BASH differs from Harshlight in the compact defect step in three important ways: (i) the outliers are calculated within an array from the replicate beads, rather than from replicate arrays; (ii) the minimum size is specified rather than being estimated from simulated data; and (iii) the compact defect step is iterated rather than being performed once. BASH forms part of the beadarray Bioconductor package.

ASSIsT / Automatic SNP ScorIng Tool

A user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software tool for SNP data visualization and inspection called GenomeStudio® (GS). ASSIsT builds on GS derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker-trait association analysis.

arrayCGHbase

New
Allows users to process microarray comparative genomic hybridization (CGH) data. arrayCGHbase contains a zoomable graphical interface that allows immediate identification of altered genomic regions and the underlying gene content by several database links. Several functions are present on this platform making possible for each user to add custom algorithms for data analysis and visualization. This webtool enables investigators to interpret single experiments and compare large data sets efficiently throughout different array platforms.

CNV-WebStore

An online platform to streamline the processing and downstream interpretation of microarray data in a clinical context, tailored towards but not limited to the Illumina BeadArray platform. Provided analysis tools include CNV analysis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritization, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases. Finally a module is provided for uniform reporting of results.