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THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focuses on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

Software package to detect different methylation levels (DMR) that gives the exact p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison.

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• SciCrunch
• 13 years ago - by Anonymous

Software for computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.

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• SciCrunch
• 13 years ago - by Anonymous

An American pharmaceutical company aiming to make a difference in the lives of people globally through their medicines, vaccines, biologic therapies and animal health products.

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• SciCrunch
• 16 years ago - by Anonymous

A set of software tools for processing raw intensity data, identifying regions of copy number variation (CNV), visualizing copy number data, and performing association analyses on a variety of copy number covariates.

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• SciCrunch
• 13 years ago - by Anonymous

SNP Analysis software for basic to advanced analyses that incorporates a number of intuitive workflows to lead you beyond single marker associations. With support for case-control and quantitative traits, whole genome and candidate gene data, you can run a breadth of statistical tests under several genetic models. Advanced regression can further help elucidate even the most complex gene-gene and gene-environment interactions.

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• SciCrunch
• 13 years ago - by Anonymous

Software for analysis of array CGH data: detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

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• SciCrunch
• 13 years ago - by Anonymous

Software program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.

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• SciCrunch
• 13 years ago - by Anonymous

Tool which can be used to identify novel miRNA gene candidates in the human genome.

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• SciCrunch
• 13 years ago - by Anonymous

Software package for importing data from Illumina SNP experiments and performing copy number calculations and reports.

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• SciCrunch
• 13 years ago - by Anonymous

Software for ultra-fast base-calling of second-generation sequencing data by blind deconvolution.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that contains functions and classes that are needed by arrayCGH packages.

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• SciCrunch
• 13 years ago - by Anonymous

Software package for dimension Reduction for Array CGH Data with Minimal Information Loss.

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• SciCrunch
• 13 years ago - by Anonymous

A software application PDF reader which provides a modified method of reading scientific papers. Different programs are available with additional information concerning the PDF, including Altimetric, Mendeley, and SHERPA/RoMEO. Related, open access articles can be saved directly from Utopia Docs and terms within the PDF can be directly searched, with results appearing within the program.

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• SciCrunch
• 16 years ago - by Anonymous

Software package for detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

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• SciCrunch
• 13 years ago - by Anonymous

Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data.

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• SciCrunch
• 13 years ago - by Anonymous

Software package to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that estimates the DNA copy number profile to detect regions with copy number changes.

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• SciCrunch
• 13 years ago - by Anonymous

Non-profit organization based out of Seattle, Washington that conducts medical research on autoimmune disease.

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• SciCrunch
• 15 years ago - submitted by Stephen Larson