Curator Dashboard

Software package that provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that uses signal-to-noise ratios (SNRs) as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set.

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• SciCrunch
• 13 years ago - by Anonymous

Narrative resource describing a visual data analysis and collection approach that takes advantage of the cylindrical nature of the zebrafish allowing for an efficient and effective method for image capture called, Specimen in a Corrected Optical Rotational Enclosure (SCORE) Imaging. To achieve a non-distorted image, zebrafish were placed in a fluorinated ethylene propylene (FEP) tube with a surrounding, optically corrected imaging solution: water. By similarly matching the refractive index of the housing (FEP tubing) to that of the inner liquid and outer liquid (water), distortion was markedly reduced, producing a crisp imagable specimen that is able to be fully rotated 360 degrees. A similar procedure was established for fixed zebrafish embryos using convenient, readily available borosilicate capillaries surrounded by 75% glycerol. The method described could be applied to chemical genetic screening and other, related high-throughput methods within the fish community and among other scientific fields.

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• SciCrunch
• 15 years ago - by Anonymous

Software package that uses a modeling strategy especially designed for normalizing high-throughput genomic data. The premise is that your data is a function of study-specific variables which are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.

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• SciCrunch
• 13 years ago - by Anonymous

Model-based software package for processing microarray images so as to estimate foreground and background intensities. The method starts with a very simple but effective automatic gridding method, and then proceeds in two steps. The first step applies model-based clustering to the distribution of pixel intensities, using the Bayesian Information Criterion (BIC) to choose the number of groups up to a maximum of three. The second step is spatial, finding the large spatially connected components in each cluster of pixels. The method thus combines the strengths of the histogram-based and spatial approaches. It deals effectively with inner holes in spots and with artifacts. It also provides a formal inferential basis for deciding when the spot is blank, namely when the BIC favors one group over two or three.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.

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• SciCrunch
• 13 years ago - by Anonymous

Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages.

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• SciCrunch
• 13 years ago - by Anonymous

Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments.

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• SciCrunch
• 13 years ago - by Anonymous

Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.

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• SciCrunch
• 13 years ago - by Anonymous

Software package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

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• SciCrunch
• 13 years ago - by Anonymous

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