Curator Dashboard

Portal for a variety of web-based, educational information sources. Subjects include biotechnology, medical genetics, digestive systems and endocrine systems. Animations require a Java-enabled browser.

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• SciCrunch
• 16 years ago - by Anonymous

Software that provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.

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• SciCrunch
• 13 years ago - by Anonymous

Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias.

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• SciCrunch
• 13 years ago - by Anonymous

Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

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• SciCrunch
• 13 years ago - by Anonymous

Software package for a Graphical User Interface for the limma Microarray package.

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• SciCrunch
• 13 years ago - by Anonymous

Software packqge for importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH (Comparative genomic hybridization) experiments.

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• SciCrunch
• 13 years ago - by Anonymous

Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data.

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• SciCrunch
• 13 years ago - by Anonymous

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